Defenders Marcelo and Morel turned strikes by Edinson Cavani and Kylian Mbappe into their own net in the 75th and 86th minutes respectively, as PSG maintained their perfect record after six league games.
PSG lead champions Monaco, who beat Strasbourg 3-0 on Saturday, by three points. Lyon slipped down to fifth on 11 points.
"It was a complicated game against a good team but we showed we could do great things together," said Mbappe, who joined from Monaco this season.
"I enjoy it a lot here, I learn a lot, I still have to improve."
The game marked the first time that none of the members of the 'MNC' (Mbappe, Neymar, Cavani) found the back of the net as Lyon proved a tough nut to crack.
Holding midfielder Tanguy Ndombele was a wall the PSG midfielders and forwards struggled to pierce and the capital side broke the deadlock shortly after the 20-year-old was substituted.
Giovani Lo Celso, who had just replaced the disappointing Julian Draxler, beat Kenny Tete on the left flank and found Cavani with a low cross.
The Uruguayan's back heel was deflected into his own net by Marcelo as PSG took a deserved lead.
Five minutes later, PSG were awarded a penalty after Ferland Mendy brought down Mbappe. As Cavani was about to take the spot kick, Neymar came to him and appeared to ask to take it. Cavani refused and his powerful shot was deflected on to the bar by keeper Anthony Lopes.
PSG rounded it off four minutes from time when Mbappe collected a nice, defence-splitting pass from Neymar and Lopes's save bounced off Morel and into the net.
(Reporting by Julien Pretot; Editing by Clare Fallon)
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