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A header from Leverkusen defender Manuel Friedrich in the 91st minute saw the hosts complete a fairytale comeback from 1-0 down to seal a valuable win which sends them top of Group E and puts them in the Round of 16.
Valencia's 7-0 rout of Genk leaves them second with Chelsea now third in the table and just one point separates the three teams.
After Ivory Coast star Didier Drogba's second-half strike had put the guests ahead, Swiss striker Eren Derdiyok came off the bench to equalise before Friedrich's dramatic winner.
With his side having lost three of their last four Premier League matches, defeat in Leverkusen is sure to pile the pressure on Villas-Boas, in his first season, as his team suffered their second straight defeat.
Chelsea must now beat Valencia at Stamford Bridge in a fortnight to go through, while even if Leverkusen lose at Genk in a fortnight, they will at least finish second in the group.
"It was an unfair result, it was heading to a draw, we had our fair share of chances, it wasn't good football by either team which was a pity," said Villas-Boas.
"It means we go to the last game against Valencia to decide our qualification.
"They are a team on the up, we will need Stamford Bridge behind us, it's in our hands. It's our responsibility and we don't want to let the fans down."
The victory was extra sweet for Leverkusen's ex-Germany captain Michael Ballack, who orchestrated the hosts' attack against his former club and had a memorable 100th Chamions League game.
"We tried to take a few more risks and felt we deserved the draw, but to go and take the victory, we are delighted," said Ballack.
Germany striker Andre Schuerrle started on the bench having battled 'flu all week while Ballack, playing with a mask to protect his broken nose, was impressive in leading the Leverkusen attack.
He headed against the bar in the first-half, then fired over after the break and was only denied by a great save from Chelsea goalkeeper Petr Cech.
Chelsea had several chances in the first-half with Daniel Sturridge and Drogba finding plenty of space to keep Leverkusen's teenage goalkeeper Bernd Leno busy.
Chelsea took the lead on 48 minutes when Sturridge's lofted ball found Drogba who turned his marker and slammed the ball into the bottom left corner.
With 19 minutes left Leverkusen coach Robin Dutt threw caution to the wind by switching defender Michal Kadlec for Swiss striker Derdiyok.
He had been on for just 93 seconds before he headed home after a super ball from Sidney Sam pulled Cech off his line and the Swiss headed into an empty net on 73 minutes.
And Leverkusen completed the fairytale when Friedrich rose highest from a corner with time almost up to cap a memorable night for the hosts.
