The hosts took their second innings from the overnight 0-0 to 70-2 by lunch and now lead by 20 runs with eight wickets in hand.
Tharanga Paranavitana, top-scorer in Sri Lanka's first innings with 72, once again held the innings together with an unbeaten 42.
Rangana Herath, who opened the innings late Sunday as a nightwatchman and played out the lone over from Mohammad Aamer, batted for an hour and 28 minutes to make 15.
The start of play was delayed by 30 minutes due to heavy early morning rain that freshened up the wicket at the Galle International Stadium.
Pakistan earned a break off the second ball of the day when Malinda Warnapura edged Umar Gul to a diving Younus Khan at second slip before a run had been scored.
Left-handed Paranavitana and Herath defied the Pakistani seamers to put on 68 for the second wicket before the nightwatchman was trapped leg-before-wicket by Younus just before lunch.
Sri Lankan captain Kumar Sangakkara walked in next and had yet to s