Thirty-year-old Karunaratne, who was 46 not out when he was hit in the back of the neck by a bouncer from Cummins, fell to the ground dropping his bat before the Australian cricketers ran for help.
Earlier, Kurtis Patterson became Australia's third century-maker of its first innings, scoring an unbeaten 114.
The 30-year-old Karunaratne, who retired hurt on 46, left the ground on a motorized stretcher.
The twin centuries also ended a drought of tons at home by Australian batsmen - 390 days to boot - going back to the 4-0 Ashes win.
Sri Lanka's new fast-bowling recruit has already represented a Sri Lankan Board President's XI, Sri Lankan Emerging Players (under-23) and Sri Lanka A.
After enduring a 2-1 series loss to India, Paine is encouraged by Australia's Ashes prospects before suspended skipper Steve Smith and deputy David Warner re-join the team.
After Cummins dismissed Dimuth Karunaratne on the last ball of the second day, he took wickets in his first two overs Saturday.
Australia lead Sri Lanka by 162 runs at the end of day two's play in the day-night Test in Brisbane.
Called into the team to replace the injured Josh Hazlewood, Richardson's first career wicket was Sri Lanka captain Dinesh Chandimal with a ball that moved slightly away from the right-hander on 5.
Patterson made 157 and 102 for a Cricket Australia XI in a pink ball match in Hobart last week.
Jhye Richardson has played seven one-days and seven T20Is so far but is yet to make his Test debut for Australia.
The Board of Control for Cricket in India (BCCI) had on Monday written to the CA refusing to play under lights after which the Australian board confirmed playing the Islanders in a day-night game in January.
Sydney: All-rounder Glenn Maxwell led a brutal Australian assault with his maiden ODI hundred as the four-time winners overcame a spirited Sri Lanka by 64 runs and inched closer to securing a quarterfinals berth in
Sydney, Jan 6: Mike Hussey fittingly guided Australia to a five-wicket win over Sri Lanka on Sunday, completing a sweep of the three-test series.Set 141 to win at the Sydney Cricket Ground, Australia reached that
Melbourne, Dec 26: David Warner smashed a quick-fire half century as Australia ended the first day of the second test against Sri Lanka at 150-3 after dismissing the visitors for a paltry 156 at tea
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