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Branco van den Boomen's free-kick gave Toulouse a surprise lead at Parc des Princes, but the champion fought back without injured duo Kylian Mbappe and Neymar.
Hakimi equalised with a sublime first-half strike and he was credited with the assist for a brilliantly taken second goal from Messi after the break.
PSG was good value for a victory that increased its advantage over Marseille at the summit and it will take some stopping in its quest to retain the title.
PSG suffered an early blow when Renato Sanches was seemingly in tears as he departed with an injury and i was rocked further when Van den Boomen sent a free-kick to the left of the wall and into the far corner 20 minutes in.
Marquinhos nodded Messi's whipped corner against the post and PSG was relieved to see the offside flag go up after Zakaria Aboukhlal thought he had headed Toulouse into a two-goal lead.
Hakimi produced the moment of quality the hosts had been lacking to level seven minutes before the break, cutting in from the right and unleashing a venomous left-foot drive that found the back of the net from 20 yards out.
The marauding Hakimi was involved in PSG's second goal just before the hour-mark, embarking on a run that that resulted in Messi firing a clinical left-foot finish beyond Maxime Dupe from outside the box.
PSG did not see the game out in convincing fashion and Mikkel Desler spurned a great chance to make it 2-2, before Messi rattled the post in a frantic finale.
