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De Villiers was caught by substitute fielder Dimuth Karunaratne off Thisara Perera one short of a 13th Test century, but his third straight half-century ensured South Africa was in control of the series opener at stumps on Day 2 at SuperSport Park.
Sri Lanka was bowled out for 180 on Thursday.
De Villiers shared a 97-run partnership for the sixth wicket with Ashwell Prince (39) as South Africa eventually broke free from a stubborn Sri Lankan bowling effort.
A 39-run last-wicket stand between Mark Boucher, who was 42 not out, and Imran Tahir (23 not out) then rammed home South Africa's advantage in the last hour of play.
Perera had 3-114 and took two early wickets as the tourists reduced South Africa to 173-5 before De Villiers and Prince came together.
Left-armer Chanaka Welegedara returned 2-87, but frontline seamer Dilhara Fernando struggled and was wicketless on the second day.
De Villiers and Prince added 84 before tea in a valuable sixth-wicket partnership as the match slowly swung back toward the Proteas, who dominated on Day 1 but were forced to work hard on a lively pitch on Friday morning.
With South Africa 90-1 overnight, nightwatchman Dale Steyn was run out in the second over of the day and Hashim Amla (18) and opener Jacques Rudolph (44) removed in an impressive, probing morning spell by Perera.
Jacques Kallis hit five fours in a commanding start, but was then struck on the helmet as he ducked into a delivery from Dilhara Fernando (1-115) just before lunch and dismissed early in the afternoon for 31.
Prince fell to Angelo Mathews (1-13) to break the crucial stand with De Villiers, but at 270-6, South Africa had re-established its advantage in Centurion in the first of three Tests after firing out Sri Lanka cheaply on a bouncy, seaming pitch on Day 1.
De Villiers hit 12 fours to continue his strong run of form after he made 64 and 73 in South Africa's last Test, against Australia at Johannesburg last month.
He drove straight down the ground and to the boundary to move to 99 but tried to cut Perera's next ball away on the off side and was caught low down by Karunaratne, who snapped up the ball just above the grass at backward point.
De Villiers preferred not to send the catch to a video review, but rather asked Karunaratne if he had taken it cleanly and walked off at his home ground after the fielder confirmed the catch was good.
Wicketkeeper Mark Boucher hit six fours to move to the brink of a half-century and No 11 Tahir had four boundaries as South Africa added late runs and pushed toward 400.
TeamsSouth Africa - Graeme Smith (captain), Jacques Rudolph, Hashim Amla, Jacques Kallis, AB de Villiers, Ashwell Prince, Mark Boucher (wk), Vernon Philander, Dale Steyn, Morne Morkel, Imran Tahir.
Sri Lanka - Tillakaratne Dilshan (captain), Tharanga Paranavitana, Kumar Sangakkara, Mahela Jayawardene, Thilan Samaraweera, Angelo Mathews, Kaushal Silva (wk), Thisara Perera, Rangana Herath, Dilhara Fernando, Chanaka Welegedara.
