Stuart Pearce's team had to win to stand a chance of securing one of the four best placed runners-up spots to make the play-offs for Denmark.
After a tense first half, a brace from Sunderland forward Danny Welbeck and Aston Villa youngster Marc Albrighton secured the victory which, given results elsewhere, secured England's passage to the play-offs.
Breakthrough: Danny Welbeck notched England's first with a typically cool finish
Pearce had named an unchanged side from the 1-0 win in Portugal, which meant Arsenal youngster Jack Wilshere had to again be content with a place on the bench.
It was a nervy opening from the Young Lions at the Weston Homes Community Stadium, and Blackburn defender Phil Jones had to make an important saving tackle as Arvydas Novikovas broke into the left side of the penalty area.
Bright future: Welbeck completed the scoring in stoppage time
The first decent opening for England came on 11 minutes when Chelsea forward Daniel Sturridge dragged his shot wide after good work down the left by Ryan Bertrand, on loan at Nottingham Forest from Stamford Bridge.
Slowly the home side started to get control of the midfield, with Lithuania picking up two quick bookings for late challenges.
Jones headed over a corner from Tom Cleverley, on loan at Wigan from Manchester United, before captain Michael Mancienne - another of the Chelsea youngsters, spending the season at Wolves - saw his long-range effort saved.
Tottenham winger Danny Rose drilled the ball just over as England continued to press for the breakthrough.
There was a let off for the home side on 35 minutes when a 25-yard free-kick from defender Mantas Fridrikas squirmed through the grasp of keeper Frank Fielding and hit the base of the post.
Welbeck dragged his 20-yard shot wide as England finished the half on top, but still unable to breakdown the stubborn Lithuania defence.
Wilshere was introduced at the start of the second half, replacing Kyle Walker and immediately England looked more assertive.
Rose had a shot blocked, while Sturridge curled his shot just wide.
The breakthrough finally came on 61 minutes when Welbeck stroked the ball into the far corner after being played through the left side of the penalty area by Wilshere's fine pass.
England knew their play-off hopes could come down to goal difference, and so continued to press.
Hero and Villain: Aston Villa's Marc Albrighton continued his excellent start to the campaign by grabbing the crucial second
Sturridge saw his neat finished ruled out by the offside flag as the game entered the final 20 minutes, before Welbeck looped his header onto the roof of the net.
The pace of Welbeck soon opened up Lithuania again and his angled shot was almost bundled into the net by a combination of keeper and defender, before, with 11 minutes left, Albrighton stabbed the ball home at the far post.
Welbeck wrapped up victory when he scored a second in stoppage time.
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