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."
Drogba's early goal came after Daniel Sturridge's long cross from the right was pulled back by ex-Valencia winger Juan Mata.
"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."
"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
