The England international grabbed the equaliser after David Villa had given Valencia an early lead, before setting up Didier Drogba's winner with a sublime pass.
The result brought back memories of the Blues' dramatic quarter-final success against the La Liga side last season when Michael Essien's last-gasp goal secured a 2-1 win for Jose Mourinho's team in the Mestalla.
But with Mourinho now part of Stamford Bridge folklore, Avram Grant had the unenviable task of lifting a Chelsea side that were held to a 1-1 draw by group minnows Rosenborg two weeks ago.
In sharp contrast, Valencia had won five of their six La Liga games this season despite not playing particularly well and won 1-0 at Schalke in their opening Champions League match.
John Terry started for Chelsea despite having surgery on a fractured cheekbone at the weekend and being forced to wear a protective mask.
Valencia started extremely brightly and almost scored inside the opening two minutes when Joaquin found David Silva after a jinking run but the striker's fierce shot was too high.
However, the hosts took a deserved lead in the ninth minute. David Villa initially lost the ball only for it to be deflected back into his path by Essien and the striker gleefully ran on to fire his shot past Petr Cech.
Joaquin should have made it 2-0 after he had combined well with Fernando Morientes only for the winger to drill his shot straight at Cech.
Almost immediately play swung to the other end where Drogba sent Florent Malouda free down the left, and when the Frenchman pulled the ball back, Joe Cole was on hand to turn the ball home from close range.
Joaquin had another great chance to score five minutes later only for Claude Makelele to get back to tackle the former Real Betis winger just before he could pull the trigger.
Silva, Villa and Joaquin were cutting the Chelsea defence to ribbons and on the half-hour Villa tried his luck from 25 yards out, but dragged his effort wide.
Chelsea were happy to go in level at the break but it was a completely different game after the interval as Valencia lost their way - their incisive passing of the first half being replaced by some nervous football.
Villa had a goal disallowed before Chelsea scored a great winner with 19 minutes left. A superb pass by Joe Cole found Drogba who swept past Raul Albiol before slotting his shot past Timo Hildebrand's despairing dive.
Valencia piled forward in the closing stages but their attacks lacked conviction and Chelsea hung on to clinch the three points that could prove crucial to their Champions League campaign and perhaps even their whole season.