The home side dominated at Anfield but goals from Nigel de Jong and Edin Dzeko kept Roberto Mancini's team in the tie until the superb Welsh striker put them to the sword.
Kenny Dalglish's team were dominant and should have won the game on the night, instead having to settle for a nervy draw and 3-2 aggregate win that was just enough to book its place at Wembley, where it will face Cardiff City.
Nigel de Jong had pulled City back into the tie by opening the scoring from distance, before Steven Gerrard leveled the score with a penalty before halftime.
Liverpool continued to press, but City goalkeeper Joe Hart was outstanding and Edin Dzeko tapped in with a goal that would have seen Roberto Mancini's team progress on away goals after extra time.
The game did not reach that stage, though, as the excellent Bellamy finally found a way past Hart in open play to seal the tie.
Bellamy started alone up front for Liverpool, with Dirk Kuyt and Stewart Downing flanking a five-man midfield and Andy Carroll forced to settle for a place on the bench.
Mancini chose to withdraw Sergio Aguero from his starting lineup, opting for a 3-4-2-1 formation that was perhaps designed to aid young defender Stefan Savic. Pablo Zabaleta and Aleksandar Kolarov filled wing-back roles, with Micah Richards shifting into the center of defense alongside Savic and Joleon Lescott.
Still, City struggled to gain a foothold in the game early on. The home midfield trio of Gerrard, Jordan Henderson and Charlie Adam efficiently controlled possession, with the visitors' three center backs particularly failing to contain the threat of the energetic Bellamy.
And the Liverpool chances came as a result.
Hart superbly denied Jose Enrique from close range, with Downing blasting the rebound high and wide, before Adam tested the goalkeeper from distance - while Bellamy did beat Hart just prior to the 25-minute mark after sneaking in behind Savic and Lescott, but the Welshman was ruled offside.
Conversely, the City threat through the first half hour was minimal. Kolarov did forge half a chance when he retrieved David Silva's heavy pass in the box, but Daniel Agger did well to clear his cross aimed at the back post.
Then came City's opener against the run of play, cancelling out the Reds' first-leg advantage.
Silva was again involved, laying on a pass to De Jong, who brilliantly curled past Pepe Reina from 25 yards while losing his footing on the slippery Anfield surface.
While City began to counterattack with more speed and confidence, the home side continued to press and dominate the ball - and moments after City's goal only a fine block by Lescott cut out a superb Adam cross from the left with Kuyt lurking.
And Adam was again the creator as Liverpool grabbed a controversial equalizer. When the 26-year-old's low cross from the right bounced out to Agger, there was little Richards could do to prevent the shot hitting his arm. Referee Phil Dowd was unforgiving, though, and pointed to the spot, with Gerrard coolly slotting home to restore his team's one-goal aggregate lead.
Liverpool had targeted the inexperienced Savic during the first half and Mancini relieved the Montenegrin center back of his duties at the break. Aguero was introduced, with City reverting to a more familiar 4-2-3-1.
A good Liverpool move down the right-hand side early in the second half allowed Kuyt to sting Hart's palms with a driven effort that deflected off of Richards, before the 24-year-old 'keeper made a second, even better save to deny Martin Skrtel, who had latched on to a loose ball in the City penalty area.
The visiting keeper's heroics did not end there. Minutes later he flung himself in the way of Downing's volley after Kuyt had broken away down the right and crossed for the unmarked English winger.
Pre-occupied with defending, City struggled to sustain any sort of attacking pressure.
Still, though, the club found another goal - again against the run of play. Kolarov charged down the left and fired in a wonderful cross that evaded Aguero but was met by Dzeko, who tapped in at the far post.
With its two shots on target, City had scored two goals and it looked on course for a smash-and-grab win at that point.
However, the visitors had little grounds for complaint when Liverpool stepped back into the lead. After receiving a pass from Kuyt, Bellamy found enough space to shoot beyond Hart after an intricate one-two with Glen Johnson.
Substitute Adam Johnson tested Reina and Dzeko had a shot from close range blocked late on but City could not find a way through and Liverpool held out for the chance to take on the Bluebirds at Wembley on Feb. 26.