A pulsating Carling Cup semi-final was heading for extra-time when Rooney struck in the 92nd minute to give United a 4-3 aggregate win and earn Ferguson a record seventh final against Aston Villa next month.
But United could face FA sanctions after City's Craig Bellamy was felled by a coin thrown from the stands in the second half as he prepared to take a corner. A full bottle of cider narrowly missed him moments later.
Under attack: City's Craig Bellamy ducks to avoid a bottle of cider thrownfrom the crowd. He had been struck by a coin
HAVE YOUR SAY. Did Man United deserve to reach Carling Cup final? Wayne Rooney's last-gasp goal fired Manchester United to victory over arch rivals Manchester City at Old Trafford on Wednesday - and booked their clash with Aston Villa in the Carling Cup final in February. But did United deserve to go through against battling City? TELL US WHAT YOU THINK Referee Howard Webb was forced to hold up the game while extra securityreinforced that corner of the ground as the tie threatened a repeat ofthe chaos that marred last week's first leg.
That match saw United's Patrice Evra struck by a lighter and the now-infamous feud erupt between Carlos Tevez and his former United team-mate Gary Neville.
Rooney's 21st goal of the season was reminiscent of Michael Owen'sinjury-time winner that gave United a thrilling 4-3 Premier League winover City at Old Trafford in September.
Ferguson said: 'Rooney's control, penetration, leading of the line, everything was terrific. That was a true world-class performance.
'I thought he was much better than he was on Saturday when he scored four goals against Hull.
'I'm delighted for our fans, too. Our support was unbelievable andwhen they are like that, you never want to let them down. The fact thatit was a semi-final added a lot of spice, and the fact that we scoredso late brought a special type of celebration. The first half was a bit cat and mouse because they sat deep, but we kept our patience, which was important.
'What we said at half-time was to keep playing our football and tokeep passing the ball around. In fairness to our players, in the secondhalf they were fantastic. Darren Fletcher was immense. He played likehe had two engines in him.'
Last action hero: Wayne Rooney wheels away after shattering City's Carling Cup dream
Tevez was on target again last night after Paul Scholes and MichaelCarrick had put United ahead, but defeat was hard to take for managerRoberto Mancini as he missed the chance to take City to a major cupfinal for the first time since 1981.
Mancini said: 'It hurts but we have another cup. We had a big chanceto reach the final but hopefully we can win the FA Cup final.
'I'm sorry for the players and supporters. But it's important theplayers go away with their heads held high. There were 10 minutes whenUnited had a lot of pressure and scored two goals. But we played wellto the end.
'I only complimented my players in the dressing-room. Andcompliments to United as well because they won. Rooney is a fantasticplayer, a top player.'
So close: Mancini saw City denied their first Wembley appearance since 1981
Scholes gave United the lead seven minutes into the second half,driving a shot into the bottom corner from 15 yards after the ball wastouched back to him by Carrick.
Carrick scored a similar goal into the same corner to put United 2-0ahead in the 71st minute as he took a pass from Fletcher and strokedthe ball beyond Shay Given. But City hit back out of the blue fiveminutes later, Tevez playing the ball wide to Craig Bellamy and thengetting in ahead of Rio
Ferdinand to steer the Welshman's cross inside Edwin van der Sar's near post.
It looked certain to force the tie into extra time and possiblypenalties until Rooney struck in the second of three added minutes.
Given pulled off a miraculous save to keep out Fletcher's header,but from the resulting corner Rooney ghosted in behind Vincent Kompanyto meet Ryan Giggs's cross and head emphatically home from close range.
Celebration: Rooney jumps on scorer Carrick's shoulders after United's second, and later sealed it
Rooney's goal made up for an awful miss earlier in the second halfthat could have killed the game off. He said: 'We were deservedwinners. We started well then went a bit slow but when we were at them,they didn't know what to do they couldn't get out.
'I wasn't worried after the miss. Maybe I should have done better,especially with the delivery. But thankfully I took the chance when itcame.'
Fletcher added: 'It was all about the team tonight. Not one playerput in an average performance and everyone was up for it. We dominatedthe second half and were so on top. City's goal came out of nothing.
When Carlos scored it took the steam out of us for a few minutes.But this was a win over our local rivals and you can hear how much itmeans to our fans after everything that went on in the first leg.'
Ferdinand played last night after pleading not guilty to an FAcharge of violent conduct over his clash with Hull striker Craig Faganon Saturday.
It means the United defender could receive a heavier punishment thana three-game ban if he is found guilty by a disciplinary commissiontoday.
Hard-fought: Rio Ferdinand clashes with Carlos Tevez
The FA may also investigate last night's missile-throwing. Bellamyheld his head in pain after being struck by at least one coin. Troublehad flared outside the ground before the game, with police making 11arrests for various offences including public order, affray andcriminal damage, to add to the 29 arrests already made since lastweek's first leg at Eastlands.
United versus Villa will be repeat of the 1994 final which Villa won3-1 through a Dalian Atkinson goal and two from Dean Saunders.
City will attempt to get over their disappointment by signing England Under 21 star Adam Johnson from Middlesbrough.
United's £10million central defender Chris Smalling signedautographs as he watched his new team-mates last night after completinghis move from Fulham.
MARTIN SAMUEL: Three-goal Tevez left in a daze by home truth Man United 3 Man City 1 (United win 4-3 on agg): Wayne Rooney finds the killer blow to end the gallant City fightManchester United 3-1 Manchester City: All the drama as it unfurledMANCHESTER UNITED FC