Firmin Mubele halved the deficit after the break, but Rennes were reduced to 10 men when Benjamin Andre picked up a second booking and Edinson Cavani netted PSG's third on 75 minutes.
He returned the favour in the 17th minute by setting up Mbappe in the box, the French worldwide doubling the tally from close range.
The result - PSG's sixth win in a row against Rennes - restores their lead at the top of Ligue 1 to nine points over second-placed Monaco.
In the 89th minute PSG had a player sent as Presnel Kimpembe was given his marching orders.
Neymar was suspended for last weekend's victory over Lille but took just four minutes to make an impact at Roazhon Park, tapping in from close range after determined work from Mbappe on the right of the box to set up the opportunity.
The 30-year-old insists he still has a very close relationship with the Brazilian despite the move
Neymar capped off a memorable performance a minute later when he tucked away another Mbappe assist, sliding in at the far post to increase his league tally for PSG to 11 goals.
The Brazil global was allowed to run in behind Hamari Traore down the left, squaring the ball with the outside of his right boot to set up another simple finish for Mbappe.
Koubek had to be alert again early in the second period, as a curling Neymar strike drew a diving save from the Czech Republic global, but Rennes halved the deficit eight minutes after the restart.
And in the 90th minute, Rennes were awarded a penalty which Wahbi Khazri missed.
Kimpembe's reckless high boot earned him a second yellow a minute from time and afforded Rennes one last chance for a consolation goal, but Khazri blasted over from the spot.
PSG almost restored their two-goal cushion in the 72nd minute but Cavani failed to convert Dani Alves' invting cross.