Filippi overtook polesitter and early race leader Max Chilton with a great move into the Ascari chicane, following the mandatory pitstops, to seal a marvellous win. He crossed the line four seconds ahead of Chilton at the end of the 30-lap event.
"It might be a year since I last drove, and it feels like yesterday, it's like time just stopped," said Filippi on the podium, his voice trembling. "The emotion feels even bigger now. My career looked finished, but now I believe in myself more than ever.
"The Coloni family believed in me, and in Italian drivers. They gave me a chance, and I gave them a return. It's an amazing team, and an amazing thing."
Meanwhile, in the title race, Davide Valsecchi pulled eight points clear over his erstwhile joint-leader Luiz Razia. Valsecchi finished sixth, after Razia spun out following contact with Fabio Leimer that left him beached on the kerbs at the Roggia chicane.
The double-whammy is that Valsecchi will start third in Sunday's reversed-grid sprint race, with Razia down in 25th.
Johnny Cecotto Jr overcame a five-place grid penalty to charge through to second for Addax, passing Chilton for the runner-up spot at the first chicane at two-thirds distance. His strategy of saving tyres in qualifying, so he could start on a new set in the race, paid off handsomely.
Marcus Ericsson further demoted Chilton in similar style a few laps later to finish third for iSport, with Racing Engineering's Leimer finishing behind Chilton in fifth. Leimer also clashed with Felipe Nasr at the Roggia, but appeared to survive both stewards' investigations into the collisions.
Behind Valsecchi in sixth, Jolyon Palmer claimed seventh ahead of Stefano Coletti - who Filippi replaced at Coloni as he moved to Rapax - Esteban Gutierrez and Julian Leal.
Third-placed man in the points, James Calado, was a lowly 12th. Front row starter Giedo van der Garde did not make it through the first corner after his car appeared to lose power right from the start.