Riot police quelled skirmishes between rival fans behind one of the goals just before kick-off in England's 3-0 win.
An English FA statement said the incidents had not taken place in the area where fans who bought tickets from the FA were located.
The cases will be dealt with on Thursday, 22 October.
"We would encourage the authorities to identify anybody involved in disorder and deal with them appropriately through the criminal system and with banning orders," the English FA said.
"We will, of course, fully cooperate with Uefa."
When fighting broke out, local police quickly intervened to form a barrier between fans to prevent the violence escalating.
Some England fans appeared to have purchased tickets for sections of the ground designated for home supporters.
Lithuania's FA has also been charged by European football's governing body over breaches of ticketing rules and for having blocked stairways.
BBC Radio 5 live reporter Alan Green reported he had seen missiles being thrown by fans.
And BBC Sport's chief football writer Phil McNulty added there had been "a few brief skirmishes between rival fans at one end of this tiny stadium where some England fans have posted themselves near Lithuania supporters".
England won 3-0 with goals from Ross Barkley and Alex Oxlade-Chamberlain, either side of an own goal from Lithuania keeper Giedrius Arlauskis.
The victory meant Roy Hodgson's side won all 10 of their qualifying matches for next summer's European Championship in France.
Uefa has charged the English and Lithuanian Football Associations over crowd disturbances at their Euro 2016 qualifier in Vilnius on Monday.