Jota put Liverpool on course for Wembley with a first half strike and he clinched their berth with a late second goal in north London.
Jurgen Klopp’s side will face Chelsea in the final on February 27.
Jota’s 13th and 14th club goals this season underlined his value at a time when Liverpool are without Mohamed Salah and Sadio Mane due to the African Cup of Nations.
The Reds, who last lifted the League Cup in 2012, are back in the final for the first time since 2016 as they aim to win the competition for a record ninth time.
It will be Klopp’s fifth cup final with Liverpool since he took charge in 2015.
In the week that Liverpool’s former chief executive Peter Robinson died aged 86, it was fitting the club returned to the final of a tournament they won four years in a row under his stewardship in the 1980s.
For Arsenal, it was a frustrating loss after they managed to grind out a 0-0 draw in last week’s first leg at Anfield despite Granit Xhaka’s red card.
Mikel Arteta’s youthful side were exposed by battle-hardened opponents, emphasising the improvements still needed to revive the Gunners.
Thomas Partey’s stoppage-time dismissal for two bookings in quick succession rubbed salt into their wounds.
Arsenal were unable to field a team when they successfully asked for last weekend’s north London derby against Tottenham to be postponed.
But Arteta sent out close to a full strength side just days later as fit-again trio Takehiro Tomiyasu, Emile Smith Rowe and Martin Odegaard all returned.
Caoimhin Kelleher replaced Alisson Becker in goal for Liverpool and quickly repaid Klopp’s faith with a superb save in the fifth minute.
Alexandre Lacazette’s free-kick was headed for the top corner until Kelleher scrambled across to tip it onto the crossbar.
But Klopp’s men cut through the Arsenal defence to take the lead in the 19th minute.
Roberto Firmino’s deft backheel found Trent Alexander-Arnold in midfield and his raking pass reached Jota on the left flank.
Cutting inside to the edge of the Arsenal area, Jota’s impudent nutmeg took him past Tomiyasu and, with three defenders arriving in a vain attempt to block, the Portugal forward scuffed a low shot that trickled past slow to react keeper Aaron Ramsdale.
Arsenal were rocked by that blow and struggled to lay a glove on Liverpool for the rest of the half.
They had a golden opportunity to get back on level terms immediately after the interval when Albert Sambi Lokonga’s lofted pass sent Lacazette clear on goal, only for the French striker to balloon his shot over the bar.
Kaide Gordon, Liverpool’s 17-year-old forward, wasted an equally good chance with a hurried close-range effort that flew high into the crowd.
Ibrahima Konate was close to putting the tie beyond Arsenal’s reach with a towering header that hit the foot of the post.
In a wide-open finale, Liverpool substitute Takumi Minamino saw his shot blocked on the line by Ben White before Gabriel Martinelli’s rising drive forced a good stop from Kelleher at the other end.
Jota made sure Liverpool would not rue those missed chances as he ran onto Alexander-Arnold’s pass and chipped Ramsdale in the 77th minute.
The goal was subject to a lengthy VAR check for offside, but Jota and Liverpool were eventually able to celebrate their place at Wembley.