The two sides had been locked together at the top before kick-off but Argentine playmaker Pastore, French football's most expensive signing, continued his fine form by embarrassing Hugo Lloris at his near post following a powerful run.
Lyon's Bafetimbi Gomis missed a great chance when his unmarked header drifted wide but PSG, who should have had a penalty in the first half, made sure of the win in stoppage-time through Christophe Jallet.
"Both sides played well," Lyon coach Remi Garde, without five first-team players, told a news conference. "Right now PSG are ahead of us but there are still 30-odd games to go."
Champions Lille are just a point behind Lyon after ending a run of five successive draws in all competitions with a comfortable 2-0 win over Stade Rennes, whom they leapfrogged up into fifth.
Moussa Sow, Ligue One's top scorer last season, settled home nerves with a seventh-minute strike following good play from England's Joe Cole and Florent Balmont flicked in Eden Hazard's free-kick just after the half hour mark.
Last term's runners-up Olympique Marseille, in good form in the Champions League but floundering in Ligue 1, could only muster a 1-1 at home with Stade Brest to lie 13th after nine games.
Andre Ayew, almost as important for Didier Deschamps' side as his famous father Abedi Pele was for Ghana, grabbed the 19th-minute equaliser at the Stade Velodrome following a well-worked move.
Romain Poyet had given Brest an early lead thanks to a mistake from home keeper Steve Mandanda and the visitors managed to frustrate Marseille throughout a disjointed game.
"We lacked the freshness to change rhythm and to put them under pressure a bit more, especially in the second half," Deschamps said.
"The situation is complicated. I hope nothing happens to my players during international week."
Montpellier and Toulouse failed to seize top spot on Saturday after a 2-2 draw at Girondins Bordeaux and 3-0 loss at Sochaux respectively, meaning they stay on 17 points with Lyon.
