Down 30-18 at halftime and still trailing 33-20 with 17:43 remaining, the Quakers (6-18, 3-4) scored nine unanswered points, six by Brooks.
Penn missed its first field goal of the second half, then went 16 of 20 the rest of the way while also making 15 of 19 free throws.
Tied at 48 with 4:44 left, Lewis and Miles Cartwright made back-to-back layups and Lewis hit a 3-pointer for a seven-point cushion.
The Big Green (6-16, 2-6) could get no closer than five thereafter.
Lewis, who had scored a combined 14 points over the Quakers' previous 11 games, was 5 of 6 from the field.
Gabas Maldunas, whose 19 points and 10 rebounds led the Big Green, surpassed 500 career points in two seasons.
Mike Brey is looking at former Notre Dame players to fill two assistant jobs that have opened up with the departures of Martin Ingelsby and Anthony Solomon.
Purdue's 2016-17 prospects got a jolt Wednesday when forward Caleb Swanigan announced he will return for his sophomore season.
Clemson's Jaron Blossomgame says he is withdrawing from the NBA draft and returning to school for a final season.