Middlesbrough rounded off their home programme in style with a double over City and a parade of the Carling Cup and FA Youth Cup after the final whistle before a near sell-out of 34,734.
It was a memorable finale for fans who have waited so long to celebrate a trophy-winning season.
The Carling Cup triumph over Bolton Wanderers in February means that Middlesbrough will be in Europe for the first time in their history.
The win over the City ended a losing three-match sequence for Middlesbrough who however will miss out on their target of a best-ever finish in the Premiership.
City have never beaten Middlesbrough in the Premiership and, apart from a period of second-half supremacy, they never looked like achieving that elusive win.
Middlesbrough took an early lead through record buy Massimo Maccarone.
The ball flew into the net from the left wing, but it looked as though the Italian had actually attempted a cross.
David James anticipated a cross and the England international was left stunned as the ball beat him at the near post.
It was Middlesbrough's first goal in four matches after losing to Wolves, Aston Villa and Liverpool.
Middlesbrough held the balance of play in the opening stages with free flowing football.
The City, however, had vociferous backing from their fans, many of whom disregarded a tannoy announcement to sit down.
Paulo Wanchope headed over for the visitors from a Michael Tarnat free-kick.
Referee Mike Riley had a quiet word with Gaizka Mendieta and Joey Barton after a tussle near the touchline.
Middlesbrough went further ahead after 32 minutes. From a Danny Mills right-wing cross Joseph-Desire Job headed the ball forward and Szilard Nemeth slid the ball into the net from seven yards.
City Manager Kevin Keegan would not have been happy with the defensive covering of his side.
Nemeth was delighted though, because his ninth goal of the season made him Middlesbrough's leading scorer in the Premiership.
City had posed little threat in the early stages, but they hit back with a well taken goal ten minutes before the break.
Paul Bosvelt gave the ball to Wanchope who turned Mills inside out and shot the far corner of the net. Australian goalkeeper Mark Schwarzer had no chance.
The goal boosted the City's confidence and Middlesbrough survived when Ugo Ehiogu blocked a Nicolas Anelka shot.
Joey Barton thought he had equalised in the 39th minute, but the goal was disallowed for a challenge on Schwarzer.
It was a debatable decision and Barton had every reason to feel it was harsh.
Maccarone tried a shot with Mendieta crying out for a pass as the interval approached.
The City survived an amazing escape as the ball ran across the goalmouth before Ehiogu shot into the sidenetting.
At the other end Wanchope blasted wide with Anelka in a good position for a pass.
Just after the break Ehiogu dallied on the ball as though expecting Schwarzer to come off his line. Middlesbrough were fortunate that this hesitancy was not punished.
Middlesbrough were losing out in midfield and manager Steve McClaren was an agitated figure on the touchline.
McClaren sent on local boy Stewart Downing and withdrew Maccarone, in a bid to strengthen the midfield.
Middlesbrough fans were restless at this stage as the City pressed for an equaliser.
Fortunately for the home side, Shaun Wright-Phillips was a having a quiet game.
Anelka shot wide with Middlesbrough's midfield over-run at this stage.
Keegan made a double substitution in a bid to pull the game round and Middlesbrough were fortunate to survive a frenetic scramble just after.
As the minutes ticked by it looked as though Middlesbrough had weathered the storm and three points were within their grasp.
Yet City could have snatched an equaliser two minutes from time. Following a Barton cross from the right wing substitute Antoine Sibierski should have done better with his far post chance.
Overall, Middlesbrough deserved their success.
Keegan was disappointed with the performance of his team.
He said: "When you give a side a two-goal start as we did it is very difficult to come back.
"I don't know whether the players thought it was just another fixture to complete. We just didn't play for the first 25 minutes. The 50-50 tackles were never won by us.
"The second half was okay, but after a very bad start we got nothing.
"I challenged my players to finish three places higher if results had gone our way. We can now only finish one place higher.
"Middlesbrough were a lot sharper and more committed. We will have to work much harder than we did today." Keegan added: "The difference between Middlesbrough and Manchester City is very little. We battered Middlesbrough at our place and even scored the goal for them.
"We should not have conceded six points to Middlesbrough." Looking ahead to next season the City manager went on: "I know there is no finance for next season. We have the players to perform but they must do better.
"It is not about finance. I am sure most of the players will feel they should have done better this season." McClaren can be more optimistic over the future.
"No-one connected with this club will forget that wonderful occasion at the Millennium Stadium when we won the Carling Cup.
"Success breads expectation and we are now expected to achieve. That is the nature of football and our supporters have every right to expect that.
"However, it is also important to make sure we don't enjoy short-success followed by long-term under-achievement.
"A number of teams in recent years have enjoyed one big season, then suddenly the expectation is to win Champions League and UEFA Cup places.
"Our aim is to make gradual progression." Unlike Keegan, the Boro boss will have cash to spend in the transfer market. Chairman Steve Gibson will again provide the financial clout to strengthen the side.
The top priority is a striker who can score 15-20 goals a season. The problem McClaren faces is where to find a striker with this pedigree.
Man of the Match: George Boateng - was a powerful midfield influence throughout the game as Middlesbrough maintained an unbeaten record against Manchester City in the Premiership over the years.