Those squandered chances came back to haunt the visitors as PSG went 2-0 up on 31 minutes when Blaise Matuidi turned in David Beckham's corner.
Ibrahimovic scored his second goal of the evening five minutes later when he found the target with a direct free kick with his right foot.
The Swedish striker almost completed his hat-trick on 42 minutes when he took an attempt on the Brest goal from outside the box, only to see it go just wide.
PSG continued to dominate proceedings in the second half as Mamadou Sakho headed Beckham's corner wide on 53 minutes and Kevin Gameiro failed to keep his header from the soon-to-retire Englishman's cross on target five minutes later.
Brest pulled one back nine minutes from time through Charlison Benschop, but it was too little too late.