Jermain Defoe scored his first international goal in four years as England cemented their spot at the top of Group F to close in on a place at the 2018 World Cup.
The 34-year-old Sunderland striker won the last of his 55 international caps in a home defeat by Chile in November 2013.
But he took 21 minutes to justify any doubters of his reintroduction, with a fine finish to open the scoring.
And his replacement Jamie Vardy netted his sixth international goal midway through the second half to seal an important three points.
Boss Gareth Southgate made three changes from the side that lost narrowly to Germany on Wednesday night, with Alex Oxlade-Chamberlain, Raheem Sterling and Defoe named in the starting line-up.
Lithuania’s game plan was apparent from the first whistle, as their rigid defensive and midfield lines were positioned as narrow as possible and stood barely 10 yards apart.
With little defending to do, full-backs Kyle Walker and Ryan Bertrand played as auxiliary wingers as England dominated possession, but for the opening quarter of the game Lithuania successfully frustrated their hosts.
Defoe got his first sniff at goal on 21 minutes, latching onto Adam Lallana’s through pass, but keeper Ernesta Setkus was off his line quickly to block.
Within seconds though, Defoe had the opener. Sterling burst down the left flank and from the byline pulled the ball back to former Tottenham marksman who, unmarked seven yards out, blasted into the top corner.
It was his 20th international goal and first since netting a brace against San Marino in March 2013.
With his tail up, Defoe tried an effort from 25 yards that he has built a career on, taking control of the ball, shifting it on to his right foot and letting fly in virtually the same movement. This time though he narrowly missed the target.
Lithuania offered very little in response, but there were hearts in mouths briefly on the stroke of half-time when an innocuous looking header forwards caught out
Joe Hart, but Arturas Zulpa’s header towards the unguarded net was hooked away by Stones.
Oxlade-Chamberlain was first to test Setkus in the second period, with a curling effort from the edge of the box that the Lithuanian stopper beat away with both hands.
With the tempo slow, Southgate turned to his substitutes on the hour and introduced both Marcus Rashford and Jamie Vardy.
Within six minutes those changes paid off as England got the crucial second goal.
After some intricate build-up play, Walker fizzed a pass into Lallana, whose deft flick breached the Lithuania backline, falling perfectly for Vardy who blasted in first time.
Eric Dier had the chance to put the game beyond Lithuania when he rose highest to meet a corner, but his header flew off target. While Rashford and Bertrand also missed the target, but England had done more than enough.
England: 1 Joe Hart (capt), 2 Kyle Walker, 5 Michael Keane, 6 John Stones, 3 Ryan Bertrand, 4 Eric Dier, 8 Alex Oxlade-Chamberlain, 7 Raheem Sterling, 10 Dele Alli, 11 Adam Lallana, 9 Jermain Defoe
Substitutes: 19 Jamie Vardy for Defoe 60, 20 Marcus Rashford for Sterling 60
Substitutes not used: 13 Fraser Forster, 23 Tom Heaton, 12 Nathaniel Clyne, 14 Luke Shaw, 15 Ben Gibson, 16 Jake Livermore, 17 James Ward-Prowse, 18 Ross Barkley, 21 Jesse Lingard, 22 Nathan Redmond
Manager: Gareth Southgate
Goal: Defoe 21, Vardy 66
Bookings: Rashford 72
Lithuania: 16 Ernestas Setkus, 2 Linas Klimavicius, 3 Vaidas Slavickas, 4 Tadas Kijanskas, 8 Egidijus Vaitkunas, 10 Arturas Zulpa, 11 Arvydas Novikovas, 14 Vykintas Slivka, 17 Mantas Kuklys, 19 Nerijus Vlaskis, 22 Fiodor Cernych (capt)
Substitutes: 6 Mindaugas Grigaravicius for Novikovas 54, 9 Deivydas Matulevicius for Vlaskis 73, 13 Simonas Paulius for Slivka 87
Substitutes not used: 1 Emilijus Zubas, 12 Edvinas Gertmonas, 5 Tomas Mikuckis, 7 Ovidijus Verbickas, 15 Arunas Klimavicius, 18 Tautvydas Eliosius, 20 Valdemar Borovskij, 21 Vytautas Luksa, 23 Rolandas Baravykas
Bookings: Vaitkunas 46, Zulpa 59
Coach: Edgaras Jankauskas
Referee: Ruddy Buquet (France)
Attendance: 77,690