While Adrien Rabiot and Julian Draxler grabbed the goals, Pastore was the orchestrator as PSG came from behind to move back to within three points of Leonardo Jardim's men, who had extended their lead at the top with victory at Caen earlier in the day.
Fourth-placed Lyon handed Monaco their only home league defeat of the season so far and threatened to similarly stun the champions when Alexandre Lacazette headed in the opener.
But Pastore created an equaliser for Rabiot and then laid on a second goal for Draxler to send PSG into the break in front after a thrilling opening 45 minutes.
The hosts could not kill the game off after the restart, though, and instead endured a nervy conclusion as Lyon sought a route back into the game but ultimately came up short.
Lyon led with just six minutes played when Mathieu Valbuena's left-wing corner was flicked on by Rafael at the near post for Lacazette to nod into the net from a yard out.
A second Valbeuna delivery, from the same side, then caused further problems for PSG, with Rafael again involved and Kevin Trapp desperately clinging to the ball after Mouctar Diakhaby had looped a close-range header against the post.
The home side initially struggled to offer a response, but, 11 minutes before half-time, Pastore forged a leveller as he made progress on the right, swapped passes with Angel Di Maria and teed up Rabiot to slot home a simple finish.
Pastore and Di Maria soon combined again and the latter forced a wonderful save from Anthony Lopes with a bending left-footed shot from 20 yards.
With PSG seemingly now in control, the visitors countered and Lacazette slipped in Memphis Depay, who rounded Trapp before going to ground inside the area as the ball ran behind. The former Manchester United man appeared to lose his footing without any contact with the goalkeeper and referee Clement Turpin waved away appeals for a penalty.
That squandered opportunity would immediately prove costly for Lyon as Pastore again conjured up an opening, with Draxler arriving in the box to meet his pass and sidefoot into the bottom-right corner.
Both sides were dealt apparent injury blows at the start of the second half, with Lacazette and Draxler withdrawn, and that contributed to a quieter spell.
Pastore remained Lyon's chief tormentor, though, and he should have had a third assist when Edinson Cavani volleyed over from the Argentina international's delicate lofted throughball.
Di Maria lashed a low strike narrowly past the right-hand post as PSG kept pushing, but they played out the final minutes wary of the visitors' speed on the counter and clinging to a one-goal lead.