Pastore broke the deadlock mid-way through the second half, with Christophe Jallet netting in the last minute as PSG proved that Qatar Sports Investments' massive summer investment has made them France's team to beat.
Despite the symbolic nature of the win, PSG coach Antoine Kombouare sought to down-play expectations after the match.
"For me, it's just a match with three points at stake," he said.
"Today we're first but there are 29 matches to go. There will be injuries and drops in form. We'll have to see how we cope with that. We'll savour this, but then we'll have to start working again."
Lyon now find themselves in third place heading into the international break, three points behind PSG and level on points with Montpellier and Toulouse.
"What made the difference was their efficiency in front of goal, and our own lack of efficiency," said Lyon coach Remi Garde.
"They're above us in the table tonight, but nothing is definitive one way or another."
Despite Lyon's ease on the ball, PSG's pace on the counter-attack gave them an edge and they procured the clearest scoring opportunities in the first half.
Hugo Lloris had to push away a shot from Jeremy Menez in the fifth minute and only an alert piece of defending from Maxime Gonalons prevented 42-million-euro ($56m) man Pastore from pulling the trigger shortly afterwards.
PSG twice went close around the 20-minute mark, with Pastore seeing a toe-poke deflected onto the post by Kim Kallstrom and Menez then obliging Lloris to save with his legs.
There were howls of derision from the home fans in the 29th minute, when Pastore tumbled under a Jimmy Briand challenge just inside the penalty area, only for referee Stephane Lannoy to award a free-kick on the edge of the box.
Lyon's best chance of the half saw Alexandre Lacazette direct a header narrowly off target, but they threatened early in the second period when Bafetimbi Gomis headed across goal and wide from Michel Bastos' deep cross.
With the intensity of the game flagging, Pastore produced a moment of class that broke the deadlock in the 64th minute.
Picked out by Mathieu Bodmer on the left, he drove past Bakary Kone and then beat Lloris at his near-post with a left-foot drive that threatened to take the roof off the famous old stadium.
Lloris intervened smartly when Pastore released Kevin Gameiro moments later, before Gomis squandered a huge chance to equalise when he headed wide from six yards after Bastos' cross found him unmarked with the goal gaping.
There were further chances for the hosts, but PSG's supporters had to wait until the 90th minute for substitute Jallet to meet Nene's free-kick with an emphatic volley and secure a cherished victory.
Defending champions Lille broke a run of five straight draws with a 2-0 victory over Rennes, but Marseille's domestic woes continued in a 1-1 draw at home to Brest.
Lille were held 1-1 at Trabzonspor in the Champions League in mid-week but they comfortably overcame Rennes through goals from Moussa Sow and Florent Balmont to climb to fifth in the table.
Despite a fine 3-0 defeat of Borussia Dortmund in the Champions League on Wednesday, Marseille have just one win to their name in nine Ligue 1 matches and sit 13th after their stalemate with Brest.
Romain Poyet gave the visitors the lead in the fifth minute with a tame shot that Steve Mandanda somehow allowed to creep underneath him, with Andre Ayew tapping home a 19th-minute equaliser from Loic Remy's low cross.
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