McCormack: Found the net
Goals from Scott Arfield, Ross McCormack and Kevin McDonald ensured Billy Stark's side moved up to second in Group 6 on goal difference, two points behind leaders Finland.
After a poor start to the campaign, Scotland have now won four straight qualifiers and have two games left to secure their place in the play-offs.
Stark's team went into Wednesday's match - held in the small industrial city of Marijampole close to the Polish border - with a game in hand over Finland and second-placed Denmark.
Scotland took control as early as the fourth minute when Falkirk midfielder Arfield opened the scoring with a header after a cross from McDonald hit the bar and wrongfooted Lithuania goalkeeper Giedrius Arlauskis.
Tomas Vysniauskas came close to levelling immediately with a shot which went close to the top right corner.
There was a blow for the visitors when Aberdeen's Charlie Mulgrew was carried off on a stretcher following a tackle in the 28th minute. He was replaced by Hearts forward Calum Elliot.
McCormack doubled Scotland's lead in the 39th minute, weaving his way into the area before finishing into the bottom corner.
A defensive lapse almost let Nerijus Valskis pull a goal back but his volley flew over the bar.
Lithuania started the second half on the front foot, Scotland forced to clear the ball off the line at one stage.
But they made the game safe on the hour mark after a goalkeeping fumble saw the ball bobble into the penalty box, allowing McDonald to poke it home.
Scotland went close to adding another to their tally in the 77th minute after Elliot blasted the ball at goal, forcing a brilliant reflex save from Arlauskis.
From the resulting corner, another heroic save from the Lithuanian goalkeeper prevented McCormack's shot hitting the back of the net.
Elliot continued to be a threat for the remainder of the match with a headed attempt from close range that beat the goalkeeper but bounced over off the crossbar.
There was confusion after the game as the Scottish Football Association denied rumours their opponents were protesting against the result.
Scotland ran out comfortable victors in Marijampole to keep their bid to qualify for next summer's UEFA Under-21 Championship finals on track.
But it later transpired they had breached UEFA regulations by arriving in Lithuania less than 24 hours prior to kick-off.
This sparked rumours after the game that the Lithuanian FA had protested to UEFA against the result.
The SFA claimed the squad's flight was scheduled to touch down prior to the 24-hour deadline but there was a delay in London.
An SFA spokesman said: "There was a delay to the flight. It went via Gatwick and there was a delay at Gatwick."
The spokesman also insisted the matter had been discussed with the Lithuanian FA, saying: "There was a one-hour meeting with the Lithuanian FA, with the Lithuanian delegate this morning.
"He didn't intimate that there would be a protest and there was no talk of a protest after the match.
"So, as far as we are concerned, no protest has been lodged and the result stands."
Any successful protest would severely damage Scotland's qualification bid were they to be stripped of the three points won on Wednesday.
The result moved them up to second in Group 6 on goal difference, just two points behind leaders Finland with two matches remaining.
The 10 group winners and four best runners-up qualify for the play-offs for next summer's finals.
Wednesday's match was Lithuania's last of a campaign in which they had garnered only one point and already stood no chance of qualifying, regardless of the result.