Goals in each half from Joleon Lescott and Edin Dzeko denied a winning end to Bolton's 2010/11 season as the Whites slipped to a 2-0 final day defeat.
Wanderers proved more than a match for their Mancunian opponents in an entertaining first half but, crucially, Roberto Mancini's men edged themselves ahead just before the break with one of the strangest goals of the season.
A ricochet off Lescott's head from a corner took the ball past Jaaskelainen, after Bolton had gone close to breaking the deadlock through a Kevin Davies header and Johan Elmander's fizzing shot.
Bolton gave as good as they got in the second half, but Manchester City grabbed their game-sealing second goal when Dzeko finished from close-range just moments after being introduced a substitute.
Results elsewhere meant that Bolton finished the season occupying 14th position in the Premier League.
Owen Coyle was forced to make one change for the final league fixture with Fabrice Muamba joining the injury list through a pulled hamstring. Johan Elmander - possibly making his final Bolton appearance - was the replacement in central midfield, while 17-year-old Josh Vela was handed a place on the bench.
The Mancunians, who brought over 5,000 travelling fans from Eastlands, could have been a goal ahead within the first five minutes had it not been for a crucial block from Zat Knight inside the six-yard box.
A slick City move cut Bolton open and when Carlos Tevez latched onto David Silva's low cross, Knight found himself in the right place at the right time to put his body on the line.
At the other end of the field, Bolton's main threat early on was from set-pieces and deliveries from Chung-Yong Lee.
After Gary Cahill had nodded a free-kick from the South Korean past the upright, skipper Kevin Davies went even closer when he towered inside the penalty box to plant a header a yard wide of the mark.
Wanderers, kitted out in their brand new home strip, enjoyed more and more possession as the first half progressed.
In typical fashion, Daniel Sturridge was leading the line and causing plenty of problems for his former employers with his pace and movement.
Halfway through the first period, Joe Hart needed to be alert to save at the feet of the on-loan striker, and from the follow-up, Sturridge put the ball on a plate for Elmander, who brought the England goalkeeper into the action again with a powerful effort from 12 yards out.
However, it wasn't all plain sailing for Hart during the first half as two lapses in concentration could have resulted in Bolton netting the opening goal of the game.
The former Shrewsbury stopper inexplicably dropped a Matt Taylor cross inside his own six-yard box and also belted a clearance straight at Elmander, with the rebound floating just over the unguarded goal.
City were in the team in the ascendency in the final quarter of an hour in the first half, and after wasting three clear-cut opportunities, they nudged themselves ahead just two minutes before the interval, ironically in freak circumstances.
Firstly Gareth Barry headed against the crossbar from point-blank range, Adam Johnson blazed over with just Jussi Jaaskelainen to beat and five minutes before the interval David Silva forced the Bolton stopper into his first real contribution of the game when presented with the ball eight yard out.
But there was nothing the Jaaskelainen could do about the deadlock-breaking strike, though, as Adam Johnson's out-swinging corner struck Joleon Lescott on the face and the ball looped up into the top corner of the net.
Bolton started the second half in a positive manner, with Cahill and Sturridge both going close in the immediate moments after the restart.
Roberto Mancini, however, made a inspired substitution on the hour mark by introducing Edin Dzeko for Johnson - and it had an immediate impact as the January acquisition doubled the visitors' lead just two minutes after his introduction.
After breaking down the left channel, Barry squared for Dzeko, who slammed the ball home from close-range, despite Cahill's best efforts.
Bolton continued to press and probe for a means back into the game and Owen Coyle made a change in central midfield as Tamir Cohen was drafted into the fray at the expense of Elmander. But with the two-goal cushion, City seemed content to keep the ball and take the pace out of the game.
Further substitutions by the Bolton boss saw the introduction of Rodrigo and Ivan Klasnic with ten minutes remaining.
Shortly after his introduction, the Croatian international blasted and effort wide of the upright, as did Sturridge, who didn't give up hope of signing-off from his loan spell with a goal.
In fact, there was to be a disappointing end for Sturridge, whose eagerness earned him a red card in the final stages for a mistimed challenge on Dzeko. Chris Foy had no hesitations in reaching for his pocket to send the 21-year-old from the field.
But even by that time, the game had fizzled out as Wanderers' nine other outfield players couldn't find a way past City's well-marshalled defence , with Mancini's men playing out the remaining minutes to secure the win that ensured them an automatic path into the group stages of next season's Champions League.
Wanderers: Jaaskelainen, Steinsson, Cahill, Knight, Robinson, Taylor (Klasnic 80), Elmander (Cohen 72), Gardner, Chung-Yong (Rodrigo 80), Sturridge, Kevin Davies (Subs not used: Bogdan, Petrov, Wheater, Vela)
Man City: Hart, Kompany, Johnson (Dzeko 60), Barry, Silva, Tevez, Boyata, Yaya Toure, Lescott, Zabaleta, De Jong (Subs not used: Given, Vieira, Balotelli, Wabara,Milner)