Scotland remain in contention for a place at Euro 2008 following second-half goals from Stephen McManus and James McFadden at Hampden.
McFadden celebrates with fellow Hampden goal-scorer McManus
A glancing header from Kris Boyd gave the Scots a half-time lead.
But Lithuania hit back when Tomas Danilevicus converted a penalty won by a dive from Hearts' Saulius Mikoliunas.
McManus got on the end of a Shaun Maloney delivery to finish from close range and McFadden smashed in a terrific strike from distance.
The result lifts Alex McLeish's side into second place in Group B on 18 points after eight games, a point behind France, who drew 0-0 with Italy in the San Siro.
Scotland pressed right from the first whistle, with centre forward Garry O'Connor using his powerful presence to unsettle the opposing defence.
Gary Teale, a surprise starter wide on the right, saw a lot of the ball in the early stages but failed to provide any meaningful ammunition for his team-mates.
Scotland should have opened the scoring on 19 minutes when Darren Fletcher's corner was headed on strongly by O'Connor and flicked on target by Boyd.
Goalkeeper Zydrunas Karcemarskas clawed the ball away from under his crossbar and it fell straight to Lee McCulloch inside the six yard box.
But the Rangers midfielder lacked composure and could only manage a weak header, allowing Karcemarskas to push the ball away.
A scrappy 10 minutes followed, punctuated by some theatrics from the visitors and bewildering decisions from referee Damir Skomina.
However, Scotland made the breakthrough on 31 minutes thanks to some smart thinking from Fletcher and Boyd.
The Manchester United midfielder caught the Lithuanians out with a quick free-kick and Boyd stooped to glance a header home from 10 yards out.
Boyd opened the scoring at Hampden
The Scots were given a lift from the goal and a surging run from Scott Brown was brought to a crude end by an ugly tackle and Karcemarskas had to get down smartly to keep out Boyd's scuffed volley.
Lithuania made a bright start to the second half, with substitute Mikoliunas making life difficult for right-back Alan Hutton.
Scotland struggled to find any passing fluency and were punished when the atrocious Skomina was duped by an elaborate dive from the Hearts midfielder.
Mikoliunas flung himself to the ground as Fletcher stuck out a leg and Danilevicus got away with sticking the penalty kick straight down the middle.
With 20 minutes remaining, McManus steered a Fletcher free kick towards the bottom corner but Karcemarskas made an excellent save at full-stretch.
The Celtic defender made an important contribution at the other end minutes later, blocking a shot from Kalonas right in front of goal.
And he was at the centre of the action yet again to fire Scotland back in front on 77 minutes.
Substitute Maloney curled in a delicious cross with his first touch of the ball and McManus crashed in at the back post to knock it high into the net with his knee.
Not to be outdone, fellow replacement McFadden improved on Maloney's contribution when he beat Karcemarskas with a wonderful shot from 20 yards.
Scotland: Gordon, Hutton, Weir, McManus, McEveley, Teale (McFadden 69), Brown, Fletcher, McCulloch (Maloney 76), Boyd, O'Connor (Beattie 76).
Subs Not Used: McGregor, Alexander, Caldwell, Hartley.
Booked: O'Connor, Fletcher.
Goals: Boyd 31, McManus 77, McFadden 83.
Lithuania: Karcemarskas, Stankevicius (Jankauskas 56), Skerla, Zvirgzdauskas, Klimavacius, Semberas, Kalonas, Cesnauskis, Morinas (Mikoliunas 47), Danilevicius, Velicka (Ksanavicius 47).
Subs Not Used: Grybauskas, Beniusis, Paulauskas, Zelmikas.
Booked: Velicka, Stankevicius, Karcemarskas, Klimavacius, Ksanavicius.
Goals: Danilevicius 61 pen.
Ref: Damir Skomina (Slovenia).
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