In a tale of contrasting fortunes for the men between the posts the Argentinian, back-up to Joe Hart, saved three spot-kicks while opposite number Simon Mignolet did not manage one as City won the shoot-out 3-1 after the match finished 1-1.
While all the focus had been on the attacking options both sides had at their disposal, the match ended up being decided by the goalkeepers.
Mignolet’s evening was something of a roller-coaster, ending on a low, as his error in allowing Fernandinho’s shot under his body handed City the lead which was only cancelled out by Philippe Coutinho’s 83rd-minute strike.
The Belgium international also made a number of excellent saves but having handed the initiative to City it was a long way back for Liverpool and their exertions began to tell in extra-time.
It was only the fourth shoot-out Liverpool had lost in 18 attempts.
Manuel Pellegrini lifted his third trophy in just under three years at the club but he will hope it is not the last - with City still in the title race and Champions League - before he is succeeded by Pep Guardiola in the summer.
For counterpart Jurgen Klopp, reaching his first final just 143 days after taking over, it was more Wembley heartache having lost the Champions League final at the venue as Borussia Dortmund manager in 2013.
Both managers made big calls in their team selections: Klopp kept faith with midfielder Lucas Leiva - who missed the 2012 League Cup triumph with injury - at centre-back in an unchanged side while Pellegrini continued with his policy of playing Caballero in cup competitions.
Lucas justified Klopp’s faith with an assured display, winning a number of important headers, while Cabellero’s greatest test was in the first minute from Alberto Moreno’s low strike.
The first real chance fell to Aguero, who has not scored in six major finals for club and country, midway through the first half when he cut inside Lucas and Mamadou Sakho, still struggling after a clash of headers with team-mate Emre Can, only for Mignolet to tip his shot onto a post.
Sakho, replaced by Kolo Toure, had to be virtually ordered off the pitch by Klopp after being determined to continue against medical advice and the France international’s frustration boiled over as he hurled a water bottle towards the bench and then hid his obvious disappointment under a coat on the bench.
The breakthrough came four minutes into the second half when Fernandinho’s narrow-angle shot from the right of the penalty area, although low and hard, went under the body of the diving Mignolet.
It provoked a wry smile from Klopp, arms folded on the touchline, who only last month rewarded the goalkeeper with a new five-year contract.
No player has made more defensive errors (five) in the Premier League this season yet this one felt like the most costly.
The game opened up as Milner shot wide, Raheem Sterling, who left Anfield acrimoniously in the summer in a £49million deal, somehow missed the target from eight yards while City were furious with referee Michael Oliver after he decided Moreno did not bring down Aguero in the area with a dangling trailing leg
With 20 minutes to Klopp gambled by taking off left-back Moreno, with Milner asked to fill in, and bringing on Adam Lallana for his first appearance in three weeks and it paid off as the England midfielder hit the post from Sturridge’s cross and Coutinho drilled home the rebound in the 83rd minute.
In extra time Mignolet went some way to redeeming himself in by brilliantly denying Aguero in a one-on-one, Caballero repelled substitute Divock Origi’s close-range header while Aguero volleyed over Milner’s attempted nod back to his goalkeeper.
Penalties followed with Caballero coming out on top, with his save from Lucas the best of his three, with Lallana and Coutinho also denied before wild scenes of celebration.