The German hit the front on Lap 24 after long-time leader and polesitter Rowland ceded top spot as energy become critical with the race drawing towards its close. Guenther had placed himself in the slipstream of the leader and was able to keep with the Nissan - which had looked very strong on home soil - while saving some usable energy for a final push.
Once Gurnther hit the front, Rowland was unable to make a move stick as hard as the Yorkshireman tried in front of a passionate Nissan support. Guenther fended off three attempts on the final lap and was able to drive to the flag to seal his and Maserati MSG Racing's first win since Jakarta in Season 9 and his fifth in the series.
RESULTS: The full Tokyo E-Prix Round 5 classification
That made it five different race winners, representing five different teams, from the opening five races - the level of competition at the top as intense as it's ever been in electric motorsport's top tier. For much of the race, no more than a second split the top three runners, while the whole pack sat within 10 seconds of one another.
Reigning champion Jake Dennis (Andretti) lined up fifth on the grid and was able to outdo the Porsches to come home third after a tasty battle between himself and Season 6 champion Antonio Felix da Costa who finished fourth ahead of teammate Pascal Wehrlein - the Mexico City winner doing enough to top the Drivers' World Championship.
Nico Mueller produced the goods in the ABT CUPRA to take sixth with prior standings leader Nick Cassidy only seventh - though the Kiwi did impressively to climb through the pack from 19th on the grid at the outset. Edo Mortara had finished seventh over the line but was later disqualified for energy overuse.
Robin Frijns followed in eighth for Envision Racing, the Dutchman in the wars but able to score. Sergio Sette Camara notched points for ERT with ninth, while Sacha Fenestraz made it two Nissans in the points with 10th.
All that means Cassidy is level on points with Wehrlein at the top of the Drivers' table while Jaguar TCS Racing hold top spot in the Teams' World Championship with 102 points to TAG Heuer Porsche's 83.
Formula E heads to Italy for a double-header and a first trip to Misano in a fortnight, 13 & 14 April.
As it happened...
Rowland held fast off the line to keep the lead with Mahindra's Mortara clambering over the back of the Nissan as he gained ground on Guenther into second. The Maserati MSG Racing driver followed third with reigning champion Dennis fourth, ERT's Sergio Sette Camara fifth and Porsche's Wehrlein sixth. Through the opening laps, less than 10 seconds split the 22-car field, with the lead three separated by less than a second.
Dan Ticktum (ERT), Sacha Fenestraz (Nissan) and Sebastien Buemi (Envision Racing) in 18th, 19th and 22nd, respectively, were the first drivers to jump for the initial of two mandatory 50kW ATTACK MODE boosts, with a choice of how to split the eight-minute total allocation in two and six, six and two or four and four minute allocations on Lap 3.
Meanwhile, Wehrlein was looking raciest in the top 10 - making it by Sette Camara's ERT for fifth at Turn 1 on the same lap, and hassling Dennis for fourth the rest of the way around Lap 3 - the Brit holding on despite being squeezed. Sette Camara was shuffled to eighth, Frijns and da Costa following Wehrlein through - and the pack behind were right on the ERT's diffuser as 10 seconds was still the gap between 1st and 22nd on-track.
Wehrlein was the first of the front-runners to jump for ATTACK MODE on Lap 8, with da Costa holding off the chasing pack to make the German's life easier - both holding their fifth and sixth positions, respectively.
On Lap 10, Rowland led Mortara and Guenther with, again, no more than a second between them. Dennis, Wehrlein, da Costa, Frijns, Sette Camara, Mueller and Nato rounded out the top 10. Rowland jumped for ATTACK, and held the lead, while Mortara followed from second - dropping down to third with Guenther profiting in the process. Da Costa also took his first 50kW boost, retaining sixth just behind his teammate.
Rowland went for ATTACK MODE two on Lap 12, allowing Guenther to inherit the lead - though the Maserati driver had yet to take either of his two 50kW power boosts. Meanwhile, Frijns got himself up into seventh spot with a move on Sette Camara, and Guenther relinquished P1 and P2 to filter into third with his first trip through the ATTACK MODE activation zone - the German did pinch second back from Mortara on Lap 14, though.
On Lap 15 of 33, it was looking good for Guenther with his race engineer relaying that he had a percent more usable energy than Mortara behind and a small advantage on Rowland out in front - that Stellantis powertrain looking tidy.
Da Costa had dispatched Dennis at Turn 15 on Lap 17, and made it by his teammate Wehrlein who was shuffled to sixth and some front wing damage. A lap later, Jaguar's 100th celebrations came to a crashing end, with Mitch Evans out in contact with Frijns in an overambitious overtaking maneouvre gone wrong.
The race fired into life from there, with Nato and Frijns, sixth and seventh on Lap 18, jumping for ATTACK MODE. Dennis was just ahead of the pair - the Brit able to help his teammate and vice versa with track position through their ATTACK MODE activations. A brief interlude came about for the recovery of some stray bodywork - the Safety Car required to clear the track, and on Lap 22 we were back green.
Dennis and Andretti timed their final ATTACK MODE activation perfectly, holding fifth with Nato doing the defending behind.
Rowland gave up track position to Guenther on Lap 24, with the Brit happy to save energy in the slipstream, aware that the Maserati driver was yet to take his second ATTACK MODE activation which should allow the Nissan back ahead.
However, Rowland could only hang on some 1.7 seconds back which meant Guenther was able to take ATTACK and hold the lead and the Virtual Race Engineer calculated that the Maserati should be able to win the race as it stood. Mortara, in third, was holding off the close attention of da Costa, Dennis, Nato and Wehrlein - with Frijns, Sette Camara and Mueller rounding out the top 10 on Lap 29. The Swiss-French-Italian had an ATTACK MODE to take, though, and filtered in fifth when he made the jump on Lap 29.
Four laps plus two added were to come, with the top three once again split by less than a second - Rowland just 0.3 seconds back from leader Guenther.
Nato took his final 50kW boost on Lap 31, and in the accordian effect, Frijns unfortunately got caught up in contact and spat out in 10th spot.
Da Costa spied a chance to jump onto the podium around the outside of Turn 15 but the reigning champion was not having any of it - feeding the Porsche wide and holding the Portuguese off on Lap 33.
Rowland did his utmost to pressure Guenther for the lead with a look around the outside of Turn 1 and the inside of Turn 3 but Guenther's Maserati looked really wide - the German on the defensive. Another sweeping move around the outside of Turn 15 wouldn't pay off as energy became ultra critical and Guenther was able to hold on for the win.