Pankratjevas took his seat for his post-match news conference and waited for the first question before announcing his resignation and walking out in less than 30 seconds.
The contest was effectively over in the first half, with England going into the interval two goals ahead, but the tie was marred by crowd trouble behind one of the goals just before kick off, with Lithuanian supporters aggrieved by the number of England fans who had tickets for the designated home end.
Riot police intervened, forming a cordon between the two groups of supporters behind Jack Butland's goal, but trouble flared up again when Barkley opened the scoring.
Police sprayed the home fans with water to force them back.
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(Reporting by Simon Jennings in Bengaluru; editing by Amlan Chakraborty)
