After a humiliating 3-2 defeat at promoted Reading on the opening day of the season, Boro left this term's Premiership's favourites shell-shocked before a 29,000 crowd at the Riverside Stadium.
What a home debut for Boro boss Gareth Southgate. The rookie manager had insisted before the game that his side could rise to he occasion despite an embarrassing performance at Reading.
There was never any chance of Middlesbrough repeating their crushing 3-0 defeat over Chelsea last season. In fact, Chelsea took an early lead and looked set for their second win of the season until Boro's storming comeback.
However, Chelsea have the talent to mount a serious title challenge despite this defeat.
The win will give Middlesbrough tremendous confidence though and lift the despondency among their fans after a quite summer in the transfer market.
The win came 20 years to the day that Middlesbrough played Port Vale in a third division game after a liquidation crisis threatened the future of the club.
Chelsea manager Jose Mourinho must have been bitterly disappointed over the failure of his side to earn three points especially after summer signing Andriy Shevchenko had given them a 16th minute lead.
Give every credit to Middlesbrough though who had no fewer than eight players from their Academy in their 16-strong squad.
Chelsea suffered an early blow when Arjen Robben picked up an injury in the warm-up and Salomon Kalou took over.
Gaizka Mendieta shot wide for Middlesbrough in the first attempt of the match.
Yakubu should have put Boro ahead but the former Portsmouth man failed to make contact with a header from a left-wing cross by Stewart Downing.
Chelsea went ahead following a brilliant move on the left. Michael Essien flicked the ball through to Wayne Bridge for Shevchenko to wrong-foot Australian keeper Mark Schwarzer with his shot. Not a brilliant finish but a decisive defence-splitting move.
Schwarzer later denied Shevchenko with a brilliant save from the Ukrainian's free-kick.
Middlesbrough were putting up a spirited display without seriously troubling Carlo Cudicini in Chelsea's goal. The visitors looked stronger in midfield, moving the ball around well.
Boro had packed their midfield and Yakubu had a thankless task as a lone striker.
During the break Middlesbrough paraded several of the players who rescued the club from liquidation and gained back-to-back promotions from the third division.
Chelsea resumed the second half with only 10 men. Didier Drogba ran on to the pitch after a minute to concede a free-kick and earn a booking for coming on without the referee's permission.
Shevchenko had the ball in the net again on the hour but a linesman had flagged for offside.
Chelsea were unlucky not to add to their lead when Frank Lampard headed against the bar from a Shevchenko cross.
Middlesbrough introduced sub Mark Viduka and the Aussie International had a tremendous impact on the result. It was a bold move by Southgate and it paid off.
There were loud appeals from the crowd when Viduka went down in the box but replays showed that referee Howard Webb was right to play on.
Then came Boro's thrilling finale. Fabio Rochemback sent over a free-kick into a crowded box where Emanuel Pogatetz gave Cudicini no chance with a powerful header.
In the 90th minute local hero Downing sent over a left-wing cross, the ball dropped for Viduka, and the Australian gleefully shot home.