The England midfielder had only been on the pitch for three minutes before he broke the deadlock with Liverpool's opening goal in the 77th minute to spur his side to a 5-1 aggregate victory.
Striker Djibril Cisse added a second with five minutes left by volleying home Luis Garcia's cross from close range.
The European Cup holders, who won the first leg 3-1 in Lithuania last week, go on to a third qualifying round tie against either SK Tirana of Albania and Bulgaria's CSKA Sofia, who play their second leg on Wednesday.
Until Gerrard's arrival as a substitute with barely a quarter of an hour to go, Liverpool had laboured to penetrate the Lithuanian champions' defence in a disappointing performance by a side showing eight changes from the first leg.
Gerrard had a free kick blocked with his first touch, set up Cisse for a chance that goalkeeper Sarunas Kilijonas saved, and then scored.
His speculative shot from the left flank flew under the body of an embarrassed Kilijonas for Gerrard's seventh goal in four qualifying games.
In a tedious first half, Fernando Morientes's header from Bolo Zenden's long throw-in in the 12th minute brought a save out of Kilijonas.
Kaunas midfielder Nukri Manchkhava warmed Scott Carson's hands with a 17th-minute free kick as both sides struggled to create chances.
Halftime substitute Cisse injected some excitement into the game with a searing shot across the face of goal following a neat touch from fellow striker Peter Crouch.
The pair looked a dangerous combination before Crouch, signed from relegated Southampton last month, was forced to leave the field with a thigh injury.
Manager Rafael Benitez's original pairing of Crouch and Morientes had failed to impress.
Despite dominating the game, Liverpool suffered a second scare when Manchkhava wasted a good chance in the 52nd minute by blazing over the bar from Sami Hyypia's miscued clearance.
Hyypia nearly made amends for his error when he headed Dietmar Hamann's corner against the bar in the 69th minute.
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