The Spaniards, still without a win in the group, led at the interval with a goal by Jonas but Andre Schuerrle levelled with a thundering drive in the 52nd minute.
Former Germany captain Michael Ballack set up Sidney Sam for the winner in the 56th to secure Leverkusen's first win over a Spanish side in the last eight attempts.
The result leaves the 2002 Champions League finalists in second spot on six points, one behind leaders Chelsea who crushed Belgium's Racing Genk 5-0.
Valencia, who had outplayed the Germans in the first half and had only themselves to blame for not having scored several more goals, stay third on two points.
"The team played a top game after the 35th minute," Leverkusen coach Robin Dutt told reporters. "The first half was not a pretty sight but then we took control.
"We managed to turn a game against a top international team and that will give us an extra boost."
MISSED CHANCES
The game, seen by both coaches as key for a top two finish that secures qualification to the knockout stage, got off to a frantic start with Valencia threatening with a powerful Roberto Soldado shot.
The Spanish forward was then fortunate to see the ball deflected into his path in the 20th minute but his close-range effort was off target.
Soldado was involved again five minutes later when he benefitted from some confusion between defenders Stefan Reinartz and Omer Toprak, cut into the area and set up Brazilian Jonas to tap in for his first Champions League goal.
Soldado should have added another a little later but failed to keep his header from six metres down before teenage Leverkusen keeper Bernd Leno made a spectacular double save as the Spaniards went on a full-frontal attack.
Frustration showed for Dutt, who was pacing up and down, barking orders. His shouts awakened his players just before the break with Schuerrle forcing a good save from keeper Diego Alves who then palmed a point-blank Ballack header wide.
Dutt brought in experienced Manuel Friedrich for Reinartz in the second half and the move paid off instantly as Valencia lost much of their first half pace.
Ballack quickly found more space in midfield and Germany international Schuerrle launched their comeback seven minutes after the restart, firing in a powerful left-footer from a Michal Kadlec cross.
With the Spaniards struggling to find a way back into the game Sam struck in the 56th, chasing down a well-timed Ballack pass to beat Alves with a curled shot.
"The result is unfair as we deserved to win," said disappointed Valencia coach Unai Emery. "I am happy for the way we played but disappointed with the result."
The two sides meet again on November 1 in Spain.
"It is now harder to qualify from the group but we have to remain optimistic. It is difficult, but there it is. We now have to beat them at home," he said.
