Pumas won for just the second time this season as Pablo Barrera scored two goals.
Jaguares, meanwhile, remained at the bottom of the ultra-competitive Group 2 and are seemingly out of playoff contention.
Jaguares had two good chances to open the score near the half-hour mark but failed to do so. On the half-hour, Christian Valdez shook off a defender and fired a shot towards the far post. The ball beat Pumas' Alejandro Palacios but rolled harmlessly past the post.
Four minutes later, Josiel Da Rocha had a free shot on goal from 15 yards out but sent it right to Palacios, who easily made the save.
It was Da Rocha again who failed to put a shot on goal as he slid in front of the goal and needed just to make contact with the ball but could not do that.
In the 42nd minute, Jaguares paid for their mistakes. Pumas' Barrera took control of the ball on the right of the penalty area and fired a left-footed shot out of Oscar Perez's reach and into the back of the net.
Two minutes later, Barrera scored his second goal of the match. Palencia had the ball on the right side of the box and lifted a ball to the top of the area. Barrera ripped a shot on goal and banged his shot in off the right post.
Pumas held on for the win and improved to 2-7-2. The defending champions are five points back of third-place Tigres and seemingly need a lot of help to get to the Liguilla, but the club still has a pulse.
For more coverage of the Mexican Apertura 2009 season, visit Goal.com's Mexican football section.