An inspired performance by Drogba and a goal from midfielder Ramires gave the Londoners the points they needed to advance and allowed coach Andre Villas-Boas the opportunity to hit back at the critics who suggested his position could be in jeopardy if Chelsea had been eliminated.
Defeat or a score draw would have consigned Chelsea to third place below Valencia but already-qualified Bayer Leverkusen's 1-1 draw away to Racing Genk meant they finished top with 11 points ahead of Leverkusen (10), Valencia (8) and Genk (3).
"It has been over the top," Villas-Boas, whose side have fallen outside the top four in the Premier League and who face leaders Manchester City next week, told reporters of the recent scrutiny of his side's dip in form.
"It is unfortunate for you guys [the media] because you have to report on a brilliant win for Chelsea.
"There is only one team in the country at the moment and that is Manchester City. I hope they qualify for the Champions League knockout stage but the attitude to them is if they qualify they qualify, if they don't they don't - we don't get that margin.
"This is a continuous persecution, it is aggression towards one club."
Chelsea were on their way once Drogba, who could well be in his final season at Stamford Bridge, fired his side ahead after three minutes and although Valencia occasionally threatened, Chelsea never remotely lost control.
In between scoring the first and third goals, Drogba made one for Ramires after 22 minutes which more or less settled the match and eased the nerves of all concerned with Chelsea who were facing elimination from the competition before Christmas after dropping points in their last two away matches.
MUSCULAR IVORIAN
Drogba's early goal came after Daniel Sturridge's long cross from the right was pulled back by ex-Valencia winger Juan Mata.
The pass found the muscular Ivorian who switched the ball from his right to left foot and fired wide of goalkeeper Diego Alves who got a hand to the ball but could not stop it going in.
Defensive hesitation by Victor Ruiz 15 minutes later allowed Ramires to poke in the second after a surging run from Drogba and Chelsea completed one of their best performances of the season with Drogba powering through and finishing skillfully for the third after 74 minutes.
"It helped that we scored so early in the game, it gave us a boost of confidence," Villas-Boas said.
"To finish top of the group is excellent, no one gave us a chance, but its a test of human character and a great win for the Chelsea players who have got respect we don't normally get and gave everybody a slap in the face."
RARELY THREATENED
Valencia, who hammered Genk 7-0 in their last Champions League match, would have qualified with a win or score draw but though they had plenty of possession either side of halftime, they rarely threatened to score, although Jordi Alba hit the outside of the post soon after Chelsea went ahead.
Valencia still played some attractive football but with little end product although goalkeeper Petr Cech was forced into a making a superb save to deny David Albelda who smacked in a sizzling long range effort after 10 minutes.
Sofiane Feghouli also brought a good save from Cech in the second half but they now will have to re-align their sights on the Europa League.
"We have to focus on the Europa League now, its a new objective and we will just have to keep fighting," said Valencia coach Unai Emery. "We did what we could, we had a lot of possesion, we created four good chances
