Kamindu Mendis, fresh from a hundred in England's five-wicket win in the first Test of a three-match series at Old Trafford last week, was the only Sri Lankan to keep England at bay before he was last man out for 74 in an innings where no other batsman made more than 23.
England's four-strong seam attack all took two wickets each, with Matthew Potts returning figures of 2-19 in 11 overs and veteran paceman Chris Woakes 2-21 in 13.
Stand-in England captain Ollie Pope, again leading the side in place of the injured Ben Stokes, opted against enforcing the follow-on, with 16 overs left in the day's play.
Blistering start
Atkinson resumed Friday just 26 runs shy of three figures after his quickfire 74 not out on Thursday added impetus to Joe Root's 143 - an England record-equalling 33rd Test century - in an overnight total of 358-7.
England, fresh from a five-wicket win in the first Test at Old Trafford last week, saw Atkinson start Friday in superb style.
He leg-glanced the first ball of the day, from Lahiru Kumara, for four and drove the second through the covers for another textbook boundary.
But to the third, he was given out lbw, only for Australian umpire Paul Reiffel's decision to be reversed by a review that indicated the ball would have missed leg stump. Atkinson, to the audible delight of a sun-drenched crowd, remained 82 not out.
Another excellent drive for four through extra cover off Kumara took Atkinson to 99.
Atkinson went to his century in storybook fashion, driving Kumara down the ground into the Pavilion for another stylish four - his 11th in a century completed in just 103 balls and also featuring four sixes.
So pure was the shot, Atkinson immediately raised his arms in celebration before the ball had crossed the rope.
A spectacular innings came to a spectacular end when Atkinson mistimed a pull off an Asitha Fernando bouncer and was brilliantly caught by a diving Milan Rathnayake as he launched himself towards the rope.
Atkinson walked off to a rousing reception, having faced just 115 balls, including 14 fours and four sixes.
Fernando ended the innings soon afterwards by dismissing Stone to secure his place on the honours boards with a return of 5-102 in 21 overs.
