The visitors were yet to open their account after nightwatchman Jack Leach faced six balls from Dilruwan Perera in the final over of the day.
Leach came in as night-watchman with one over left to negotiate, which he safely did, playing out a maiden to see England through to the close.
Akila Dananjaya, who was reported by the match officials for a suspect bowling action during the first test, put the controversy aside to dismiss opener Rory Burns in his first over. Next time we will study the fielder before taking that run. With Nos. 9, 10 and 11, he put on partnerships worth 41, 56 and 28 respectively, placing Sri Lanka in a position of some strength when they had seemed likely to concede a significant first-innings lead.
Sri Lanka, who started the day at 26/1, posted a total of 336 after batting through nearly the entirety of the second day.
"We're a little bit disappointed that they've got a lead", England spinner Jack Leach said. Stand-in skipper Suranga Lakmal was unbeaten on 15 at the end. "But we're feeling good about bowling last on that wicket".
A partnership of 96 between Dimuth Karunaratne and Dhananjaya de Silva had frustrated England's bowlers for much of the morning but with just 20 minutes until lunch, they tried to sneak a quick single only for Stokes to throw down the stumps and send Karunaratne on his way.
"If we can get England before 250 it will be a gettable target for us", he added.
The incident occurred during the third session of play on Thursday with the on-filed umpires deeming Roshen Silva for a deliberate short run.
Welcome! Day 3 of the Pallekele Test is upon us and fair to say that Sri Lanka are ahead at this stage.
'That's going to give us a great chance'.
Silva, Karunaratne and De Silva will regret not converting to triple figures, as was the case with Curran and Buttler before them.
After Pushpakumara's ugly heave to mid-wicket, Karunaratne and De Silva stayed together for 146 deliveries, repelling all three of England's frontline spinners as well as three exploratory overs from captain Joe Root and a brief burst from James Anderson.