"It was difficult against a team that hadn't lost at home yet this season," said PSG's coach Luis Enrique.
"We got off to a very good start...The second half was the worst I've had with PSG, Brest were better."
Nonetheless, PSG saw off early-season surprise package Brest thanks to a brace from Mbappe either side of half-time and a Warren Zaire-Emery rocket.
The late win allowed PSG to keep pace with fellow top-of-the-table sides Nice and Monaco and they now sit second in the league on 21 points, one point behind leaders Nice.
Wonderkid Zaire-Emery, 17, gave the travelling side the start they wanted on 16 minutes when he rifled a fine strike into the top corner from distance, following fancy footwork in the build-up from Bradley Barcola.
PSG's lead was then doubled on 28 minutes when Mbappe was released by Lee Kang-in before finishing in a style reminiscent of his strike against AC Milan last Wednesday.
Brest looked to be heading into half-time trailing by two until Steve Mounie found himself all alone in the box two minutes before the break and he punished PSG.
Energised by the goal before half-time, Brest got back on terms thanks to a Jeremy Le Douaron header in the 52nd-second minute, which appeared to be enough to ensure the points would be shared evenly.
However, a recently revitalised Mbappe stepped up in the 88th minute to claim all three points for PSG, converting after his penalty was saved.
"I don't know if we deserve it because they also had chances and we took risks. At 2-2 we had chances that we couldn't convert," said Brest coach Eric Roy.
On Friday, Nice moved into top spot with a 1-0 win away to 17th-placed Clermont courtesy of a second-half Hicham Boudaoui goal.
Leading the table heading into the weekend, Monaco will want to move back into first place on Sunday when they travel to Lille.
