Joining Barca and Bayern into the knockout stages were Valencia and Shakhtar Donetsk while Celtic still have work to do to book their ticket after defeat at Benfica.
Frustratingly for Chelsea their fallow spell in the Premier League spilled over to Turin where Roberto di Matteo\'s men were swept aside 3-0 by Juventus.
With Shakhtar seeing off Danish minnows Nordsjaelland in Copenhagen the Londoners slipped to third in Group E, with their fate now out of their hands going into the final roll of the group stage dice next month.
"Last season the Champions League was like a dream, now this is like, not a nightmare, just very disappointing," said Chelsea keeper Petr Cech.
He added: "We said before the game that we have our destiny in our hands, not any more. Now we need to do our bit, we need to win our last game and hope our fate is kind.
"Being realistic Juventus played very well and they need a point and Shakhtar are already through. It is a very sad moment."
Barcelona kept the wheels firmly on their pursuit of a fourth European crown, bouncing back from defeat at Celtic in their last run out to see off Spartak Moscow 3-0 in the Russian capital.
Lionel Messi was the hero of the night, scoring twice and setting up Dani Alves for the opener to maintain Barca\'s control of Group G with 12 points.
Messi, who moved level with Ruud van Nistelrooy on 56 Champions League goals but behind Raul, the competition\'s all time scorer with 71, was as unassuming as ever after the game.
"My aim was just to get the ball, create chances and that we win the game, that is what is important," said the Argentine icon.
"We knew we couldn\'t afford to make mistakes after what happened against Celtic and that we had to go out strongly even though it is difficult to play away in this competition."
Barca had lost their previous away match at Celtic 2-1, despite dominating possession but were unable to make the most of their chances.
"Against Celtic we had the same number of opportunities but sometimes they go in and sometimes they don\'t," said coach Tito Vilanova.
"Everyone talks about Leo, the goals and the records but it is more his awareness and tactics. The way he defends and attacks and helps the team in all areas."
Barca qualify as Group G winners on 12 points, with Celtic and Benfica fighting it out for the all-important runners-up spot with both teams on seven points after the Portuguese side\'s 2-1 win in Lisbon.
In Celtic\'s favour however is the fact that in the closing games Benfica are at the Nou Camp to take on Barca while Celtic have a potentially easier assignment against already eliminated Spartak.
"I\'m disappointed with the two goals we conceded. There was a lack of composure, a nervousness about us at times on the ball. It is a young team and this is a difficult place to come and play football," manager Neil Lennon said.
"We have one more crack at it against Spartak and we live to fight another day," added the Northern Irishman.
In Group F, Valencia took to the pitch against Bayern in the happy knowledge that they were through to the next round as a result of Lille\'s earlier 2-0 win at BATE Borisov.
A 1-1 draw in Spain earned Bayern qualification from the group as well.
Midfielder Sofiane Feghouli had put Valencia ahead with time running out, but Bayern held their nerve as Germany midfielder Mueller netted the equaliser.
In other action a youthful Manchester United lost 1-0 at Galatasaray in a \'dead\' game with United having already assured themselves of top spot in Group H while Cluj went second on the back of a 3-1 win over Braga.