The Portugal international's tame shot found its way through a sea of Arsenal bodies in the first half before his dinked effort over Aaron Ramsdale in the second 45 was given following a VAR review.
Arsenal started on the front foot against the Reds after last week's goalless first leg but failed to properly test Caoimhin Kelleher in between the sticks, and Liverpool had a goal of their own ruled out for offside through Joel Matip.
However, Jota span the returning Takehiro Tomiyasu - who endured an off night for the Gunners - before his scuffed effort wrong-footed Ramsdale and trickled over the line in the 19th minute.
Jurgen Klopp's side began to assume control of the game following the opener, but the visitors then witnessed 17-year-old Kaide Gordon spurn a magnificent chance to make it two as his close-range effort sailed over the bar.
Liverpool would grab that insurance goal, though, as Trent Alexander-Arnold found Jota with a long ball after Gabriel Martinelli's slip before the former Wolverhampton Wanderers man chipped the ball over the onrushing Ramsdale with 13 minutes remaining.
The Reds' celebrations were initially halted by the offside flag, but VAR awarded the goal, and Arsenal's evening went from bad to worse when substitute Thomas Partey saw red for two bookable offences.
Liverpool will now do battle with Chelsea for the 2022 EFL Cup Crown at Wembley on February 27. body check tags ::