Samaraweera, a 33-year-old veteran of 60 Tests, reached his hundred in the last over of the morning session, courtesy of an overthrow that fetched the batsman five runs.
Top-ranked India are seeking a series-levelling win after losing the first Test by 10 wickets. The second Test was drawn.
The overnight pair of Samaraweera and Angelo Mathews batted for an hour to take their fifth-wicket partnership to 89 runs, when India finally broke through.
Mathews, who made 45, was trapped leg-before by Pragyan Ojha, giving the Hyderabad left-arm spinner his third wicket in the innings.
Ojha struck again six overs later when Prasanna Jayawardene, who made nine, missed an attempted sweep and was caught plumb in front of the wicket.
Ojha was the lone Indian bowler to take advantage of a wicket assisting turn and bounce, returning to lunch with figures of 4-97 from 39 overs.
Leg-spinner Amit Mishra, who replaced the injured Harbhajan Singh, proved expensive with 0-121.
