Substitute Jamie Vardy was also on target for Gareth Southgate's side in a one-sided, dreary victory that kept England top of qualifying Group F with 13 points from five games.
It was hardly an emphatic peformance against a side ranked 93 places lower than England in the FIFA rankings and Southgate was right to say he would not be eulogising about it.
He heaped praise, however, on the 34-year-old Defoe who, three and a half years after his last cap, became the sixth oldest player to score for England when he pounced for his 20th international goal in the 21st minute.
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"He was thrilled to be back in the squad and his professionalism has been great for some of the younger players to see," Southgate told reporters after his first competitive game since being named as full-time manager in November.
"I would have put my house on him scoring at some stage today. He has had a really positive impact on everybody."
After earning plaudits for their bright play in a 1-0 friendly defeat by Germany in midweek, England were expected to rout Lithuania but plodded along for the first 20 minutes, failing to test Ernestas Setkus's goal despite overwhelming possession.
It took Defoe, back in an England shirt for the first time since November 2013, to inject some spark.
He went close when latching on to Adam Lallana's clever reverse pass to force a fine save from Setkus.
Then he fired England ahead with a typically sharp finish after Raheem Sterling's burst of acceleration down the left saw the Manchester City forward deliver an inviting cut back.
The lively Defoe flashed another snap-shot just wide but England toiled away bluntly against Lithuania's yellow wall.
The hosts had a scare on the stroke of halftime when a clearly offside Nerijus Valskis headed towards an open goal under pressure from goalkeeper Joe Hart but his weak effort was cleared off the line by a retreating John Stones.
Lithuania had a half-chance after the break when Vykintas Slivka's deflected shot was comfortably gathered by captain Hart.
England responded with Alex Oxlade-Chamberlain's 25-metre effort clawed away by a flying Setkus.
Defoe then made way for Vardy - with Marcus Rashford replacing Sterling - and the Leicester City striker made an instant impact, scoring with a neat finish from Lallana's pass.
"It was a case of job done," Southgate said.
"We'd have liked a bit more but only one team came to win the game and it's always difficult to break down a packed defence as we did."
(Reporting by Martyn Herman; Editing by Ken Ferris and Ian Chadband)
