The Three Lions needed a first-half penalty from Harry Kane to make it four wins in a row for the first time since October 2015, but it was another dreary display from Gareth Southgate's side and they came away from the match fortunate to have picked up all three points.
Having clinched qualification despite an uninspiring performance in their 1-0 win over Slovenia on Thursday, Southgate made seven changes to his side including debuts for Harry Maguire and Harry Winks and a return from suspension for Dele Alli.
Maguire almost marked his maiden cap with a goal inside five minutes only to be denied a sitter by the faintest of touches from a Lithuanian defender, before Kane had his first sight of goal when he flashed a long-range effort wide of the target.
It was the home side - ranked 120th in the world - who fired the first serious warning shot, however, as a slip from Maguire on the artificial pitch allowed Darvydas Sernas space to flick an effort towards goal which rippled the side-netting on its way behind.
Southgate's side did soon up the tempo, though, and Michael Keane flashed one shot narrowly wide from the edge of the box before the opening goal arrived from the penalty spot just two minutes later.
Alli was brought down inside the area to leave referee Orel Grinfeld no choice but to point to the spot, and the in-form Kane made no mistake by tucking his finish in off the post from 12 yards for his 15th goal since the start of September.
Marcus Rashford was another of the four players to keep their place in the starting lineup from Thursday, and he almost doubled England's advantage with seven minutes remaining of the first half when he skipped past two defenders before drawing a low stop from the keeper.
Lithuania were not completely out of the game themselves, though, and they came close again in the final stages of the half when Fedor Cernych's snapshot from outside the area had Butland worried as it bobbled past the post.
The home side's hopes of a famous result grew even further in the second half when Sernas latched on to a loose ball deep inside the England half, but he couldn't keep his shot down from just outside the area.
Winks was then denied a debut goal by Ernestas Setkus, but England almost fell behind moments later when Butland needed to pull off a fine fingertip stop to deny Keane from turning the ball into his own net.
Lithuania could have easily been level by that stage as England struggled to turn their possession into chances despite the relatively poor level of opposition, and the home side created another clear chance shortly past the hour mark when Sernas sliced an effort well off target at the end of their best move of the match.
Southgate's side did begin to get a little more joy in the final third during the final 25 minutes, but Alli, Aaron Cresswell, Kane and Sturridge all failed to make the most of chances to double England's lead.
Lithuania almost punished the visitors for their lethargy with another chance just six minutes from time, but Deivydas Matulevicius fired straight at Butland as England survived another scare.
Both Sturridge and Maguire missed opportunities to add a second for England in stoppage time, but it would have flattered the visitors and in the end they were fortunate to come away with the win at all having given up at least as many clear chances as they created against a team ranked below the likes of Lebanon, Rwanda and Bahrain.
The result means that England end the campaign eight points clear of Slovakia, who narrowly beat Scotland to the playoff spot on goal difference, although Southgate will know that significant improvement is still needed ahead of next month's friendlies against Germany and Brazil.