The Olympic team gold medallist edged out his London 2012 team-mate Nick Skelton in thrilling fashion during a 10-rider jump-off at the Olympic Park.
Maher, going last aboard Cella, knocked more than a second off the time Skelton had clocked with Big Star in a thrilling finale to the event.
"My first fast round was the difference between winning and losing. I had nothing to lose," Maher said. "To get on the podium you had to take every risk and for me it was winning or nothing.
"Normally I don't hear the cheering in the crowds but like the Olympics I did today."
Just behind the British pair - a hundredth of a second off - was world number one Christian Ahlmann, riding Taloubet Z. The German was the only rider to break up British domination of the top five; William Funnel with Billy Congo and Scott Brash on Hello Sanctos grabbed fourth and fifth respectively.
Portuguese Luciana Diniz atop Winningmood and Frenchman Patrice Delaveau with Lacrimoso 3 HDC had to settle with sixth and seventh despite, like the five riders above them, also recording three perfect rounds.
Diniz heads the overall standings, with Michael Whitaker the top-placed British rider in sixth.
The GCT next visits the shores of the Mediterranean, in Cannes from June 13 to 15, for the fifth of 13 legs, before heading to Monte-Carlo from June 27 to 29.
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