Holding a 1-0 advantage from the first leg of the play-off in Romania the hosts coasted through in front of their own fans at Eastlands.
Shaun-Wright Phillips made the breakthrough and Dedryk Boyata extended their lead with his first goal for the club.
Manager Roberto Mancini rang the changes and kept only four of the side that started in the 3-0 victory against Liverpool on Monday.
Vincent Kompany was named captain while goalkeeper Joe Hart, Micah Richards and Nigel De Jong were also retained.
Despite switching things around Mancini was still able to call on two World Cup winners in Spain's David Silva and France's Patrick Vieira.
City got off to a flying start with De Jong racing forward before firing in a shot that brought the best out of goalkeeper Costel Pantilimon.
That set the tone and Timisoara were again forced on the back foot in the 12th minute when Jo showed good footwork but dragged his effort wide of the post.
Jo, who appears to have won favour with Mancini after loan spells with Everton and Galatasaray, was partnered up front by Emmanuel Adebayor.
City kept up the pressure and almost opened the scoring in the 37th minute. Silva delivered the ball from the left and Jo peeled away from his marker to get in a header.
However Pantilimon reacted brilliantly to push the Spanish forward's effort over the bar and prevent his side going further behind on aggregate.
Then Adebayor squandered a good chance when he evaded a couple of challenges and skipped into the penalty area, only to send his effort the wrong side of the post.
City eventually got their reward in the 42nd minute and made it 2-0 on aggregate with a fine move.
De Jong picked out Vieira and he split the defence with a glorious through-ball to Wright-Phillips.
The England winger, who started on the bench against Liverpool, had little hesitation in rattling a shot beyond the goalkeeper.
Timisoara, however, had not given up and won a corner in the 55th minute. Mircea Axente got away down the right and Boyata took no chances, putting the ball into touch.
Cosmin Contra sent his delivery into the area but Jo showed his defensive side to head clear.
No sooner had he done that than the Brazilian returned to his attacking duties only to see his shot smothered by the goalkeeper.
City made it 2-0 on the night and 3-0 on aggregate in the 59th minute thanks to Boyata.
The 20-year-old defender climbed high at the back post to thump a header into the net following a free-kick from Silva and savoured the moment after a fine finish.
That goal sparked a fierce spell of pressure from City in the space of a few minutes.
Adebayor should have scored following a dreadful backpass by Ovidiu Burca but somehow the former Arsenal striker clipped his shot wide.
Then Silva saw his effort blocked before Jo sent a header off target as the visitors began to wilt.
It was becoming little more than a training exercise with City spraying the ball about and keen to build on their 3-0 advantage.
Silva cut inside and fired in a shot that Pantilimon did well to push high into the night air.
Timisoara held out in the final few minutes while City will look forward to the draw and the next stage of their European adventure.