The Spanish side had already qualified for the last 16 but sealed top spot with a Lionel Messi strike and Gerard Pique's clever second.
Pique stabbed into the bottom corner in what looked like a planned move from Messi's swept delivery, after the Argentine fired home through a crowd.
Luuk de Jong scored a late consolation for PSV, who missed a host of chances, reports BBC
After the game, Pique said that the build-up to his goal was "practiced", but Messi later suggested there was an element of luck involved, as he denied the defender's claim.
"It was not rehearsed," Messi said. "That's a lie.
"It was a badly taken free-kick, Pique was there and the goal was just lucky."
The Dutch side hit the frame of Barca's goal four times before finally finding the net, with the five-time European champions repeatedly exposed at the back.
It led to a nervy end to the match for Barca, and Denzel Dumfries had a strong injury-time penalty shout turned down after Clement Lenglet appeared to catch him in the box with a clumsy challenge.
With one fixture to go, Barca lead second-placed Tottenham by six points, with Spurs ahead of Inter Milan on goal difference,
Their final match of the group stage is at home to Mauricio Pochettino's side on Tuesday, 11 December, when Inter host bottom side PSV.
