Karunaratne, fresh from a match-winning century in the first Test in Galle last week last week, hit six boundaries during his 100-ball stay in overcast conditions.
The first session of the game was washed out due to rain and play will begin at 1:40 pm (0810 GMT). A possible 60 overs are planned for the day with extended time.
The 29-year-old opener was struck by a throw-down from ex-England international Marcus Trescothick, working with the team in a temporary coaching capacity, during practice on Tuesday.
The England and Wales Cricket Board releases the international fixtures for next season on Wednesday, with a packed programme featuring visits by the West Indies, Australia, Pakistan and Ireland.
In contrast, the West Indies have gone off the boil since dominating England in the home series in the Caribbean six months ago and then going toe-to-toe with the same opponents in the subsequent ODI series.
World Cup winner Archer, who replaced the injured James Anderson in England's team for the second Ashes Test, took five wickets in the drawn match, including 3-32 in Australia's second innings on Sunday.
Labuschagne was not confirmed as playing until Sunday morning when Australia star Steve Smith was ruled out with concussion, having been hit by a Jofra Archer bouncer during his 92 on Saturday.
At lunch, England were 157-4, a lead of 165 runs, with Stokes (51 not out) and Buttler (31 not out) having so far shared an unbroken stand of 86.
The star batsman collapsed face forward after a sickening blow to the side of the neck and head when on 80 during Australia's first innings of the second Ashes Test against England on Saturday.
Karunaratne posted his ninth Test hundred along with enjoying a record-equalling opening partnership of 161 with Lahiru Thirimanne, who made 64, as Sri Lanka collected their first points of the World Test Championship.
England were 96-4 in their second innings -- a lead of 104 runs -- when rain forced an early close on Saturday.
Afghanistan arrive later in August for their maiden Test against Bangladesh in Chittagong from September 5.
He was expected to confirm his retirement thoughts after the recent World Cup in England and Wales where he claimed just one wicket in eight matches.
No team have successfully chased more than 99 runs at Galle, giving the visitors hope they can be victorious at the ground for the first time ever after three previous losses.