Fighting broke out before the national anthems when locals took exception to the large number of England fans who had bought tickets in Vilnius for the designated home end. Riot police intervened, forming a cordon between the supporters and penning the Lithuanian fans into the corner of the end behind Jack Butland's goal, only for trouble to flare again when Ross Barkley opened the scoring.
Police sprayed the home fans with water to force them back.
The tension eased, with England far from flustered on the pitch as they ran out comfortable 3-0 winners - with an own goal from Giedrius Arlauskis and Alex Oxlade-Chamberlain's effort settling proceedings.
England are the sixth team to achieve 100 per cent success in a European Championship qualifying campaign, winning all 10 games in Group E, scoring 31 goals and conceding only three.
NEXT STEP FORWARD
It would have been a surprise if we had not qualified. But the friendlies are against better, stronger opposition sides. We'll see how we deal with that.
ROY HODGSON, England manager
While they have not confronted particularly daunting opponents, Hodgson welcomed the recovery from the ignominy of Brazil, where they exited at the group stage.
"I did believe the team could go unbeaten," he said. "I'm not trying to change perception of the World Cup because we didn't get out of the group, lost the first two games and that finished us off.
Three Lions' three talking points
Spain, France friendlies better gauge of progress
Roy Hodgson's side made history in Vilnius by ensuring they won all 10 of their qualifiers to secure passage to the European Championship with a pristine record for the first time.
Yet what did that actually prove?
The manager put the winning sequence into context by suggesting he may learn far more from the prestige friendlies against Spain and France next month.
England are just the sixth team to achieve a 100 per cent record in qualifying and only two of those - Spain and Germany, the winners and semi-finalists at Euro 2012 - went on to make a real impact in the tournament proper.
The worry for Hodgson is that his own developing team are more likely to emulate France and the Czech Republic, at Euro '92 and Euro 2000 respectively, by failing to emerge from their group at the finals.
Final qualifier was audition for best of back-ups
This side was very much a reserve line-up, boasting a combined 140 caps before kick-off and an average age of 24.7. The involvement of Kyle Walker, Jack Butland and Danny Ings swelled the number of players used in the qualifying campaign to 33.
Quite how many would be in contention if the walking wounded were restored to fitness remains to be seen.
The regular back-line were resting. Alex Oxlade-Chamberlain and Adam Lallana are favourites of the manager. The former scored while the Liverpool player's fine touch helped conjure the second goal. Ross Barkley glided through the contest impressively enough.
But if Jack Wilshere, Jordan Henderson and James Milner are fit, they would presumably be Hodgson's preferred midfield trio.
This was an audition to determine who should be considered the best of the back-ups.
Shelvey deserves another chance against Spain
So how does one make a proper judgment on Jonjo Shelvey's prowess at this level, having seen him confronted by opponents of this standard?
Lithuania offered so little thrust through the centre that the Swansea midfielder could afford to stroll around, picking up loose balls and distributing possession without ever feeling flustered.
Yet, on the basis that Wilshere and Michael Carrick have proved particularly injury-prone, Shelvey might imagine he can play that deep-lying role Hodgson so favours when Euro 2016 begins.
The worry is that better opponents might flood through a midfield this forward-thinking, so Hodgson should offer the 23-year-old another run-out against the Spanish to see how he copes when quality players gallop at him.
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"But I felt it could be an experience which serves us in the future because we never want it to happen again.
"Targeting going unbeaten was a big goal to set but something in me said we had good players here, and we're not dependent upon just 11."
Hodgson, whose opposite number Igoris Pankratjevas resigned after the match, praised the scoring contribution and continued development of Barkley in a radically altered team to the side who beat Estonia on Friday.
Hodgson hopes to learn more about his squad's development since the World Cup in next month's friendlies against Spain and France.
"We will use those games to learn where we are," he said.
"If we concentrate and play properly, we can do well.
"It would have been a surprise if we had not qualified. But the friendlies are against better, stronger opposition sides. We'll see how we deal with that."
Everton defender Phil Jagielka, who captained England in the absence of Wayne Rooney, Joe Hart and Gary Cahill, is also looking forward to the opportunity to see how England measure up to some of Europe's elite.
"We have chosen some really tough friendlies. It will be hard games but we will try to prove ourselves," he said.
"The gameplan from day one was to win all 10 games and we have done it. We have good youth coming through and, hopefully, if we can nurture it, we could have something special."
Tottenham teenager Dele Alli was a substitute on Monday and now has almost as many England caps (two) as starts in the English Premier League (four).
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