Trailing 2-1 after last week's bad-tempered clash at Eastlands, United turned the tie on its head with goals from Paul Scholes and Michael Carrick, only for their former striker Carlos Tevez to level it for City.
But with the aggregate score 3-3 and extra time looming, Rooney's 21st goal of the season crushed City's bid for a long overdue trophy and sparked ecstatic celebrations inside a crackling Old Trafford.
Holders United will take on Aston Villa at Wembley on February 28, a repeat of the 1994 League Cup final which Villa won 3-1.
It was the seventh time manager Alex Ferguson has taken the club to the League Cup final, while City's long wait for a first trophy since the 1976 League Cup continues.
It took until the second half for the match to come to the boil after a frenetic opening period in which Tevez, scorer of two goals in the first leg and booed by United's fans, came closest to scoring with a diving header.
A yellow card for Tevez for a foul on Rafael stoked the atmosphere and United went in front after 52 minutes with a clinical finish by Scholes.
The goal seemed to suck the belief from City's players and they were on the ropes with 20 minutes to go when Carrick's precise finish after being teed up by Darren Fletcher put United ahead on aggregate.
Rooney should have buried City when he somehow missed the target from inside the six-yard area and that looked costly when Tevez pounced, cleverly flicking in Bellamy's cross with the outside of his right boot. Shay Given produced a superb save to deny Fletcher but could do nothing when Ryan Giggs curled in a magnificent cross which Rooney nodded in.
Chelsea back on top
Chelsea, meanwhile, returned to the top of the Premier League when they convincingly beat Birmingham City 3-0 at Stamford Bridge.
Two goals from Frank Lampard and one from Florent Malouda lifted Chelsea to 51 points from 22 matches.
Arsenal had a chance to go top if they had matched or bettered Chelsea's performance, but they were held to a goalless draw at Aston Villa and slipped to third with 49 points from 23 games. Manchester United fell to second with 50 points from 23.
