The German beat his British rival Jake Dennis (27), driving for Porsche-powered Avalanche Andretti and making more overtakes than anyone else, by 1.252 seconds in a repeat of Friday's top two at the Diriyah street circuit.
Rene Rast (36) took third, after fending off Jaguar's Sam Bird (36) in the late stages, to put newcomers NEOM McLaren on the podium for the first time.
British rookie Jake Hughes (28) had earlier secured McLaren's first pole position, in only his third race for the team that won the title under Mercedes ownership last year, but finished fifth after running low on power at the end.
"Our race pace is incredible, again today we had the perfect strategy," said Wehrlein, who started fifth on the grid and became only the fifth Formula E driver to win both races in one weekend.
"This weekend will be one I will never forget," added the former Formula One driver, who finished second to Dennis in this month's Mexico City opener.
The result meant Porsche powertrains have finished one-two in every race so far this season.
Wehrlein now has 68 points to 62 for Dennis, with Envision Racing's Sebastien Buemi (34) a distant third on 31.
