Sangakkara was unbeaten at the break on 51 with skipper Mahela Jayawardene on five not out after Sri Lanka won the toss and opted to bat on a flat pitch.
Warnapura earlier steadied the innings with a brisk 48-ball 59 to help his team recover from the early loss of debutant opener Tharanga Paranavitana, who was dismissed for a first-ball duck.
Pakistan's frontline paceman Umar Gul struck with the fourth ball of the innings when he forced left-hander Paranavitana to edge into the slip where Misbah-ul-Haq took a smart catch.
Warnapura and Sangakkara added 90 for the second wicket before first-change Yasir Arafat provided the breakthrough.
Warnapura, who hit nine boundaries, edged Arafat to Haq who held a low catch in the slip.
The 32,000-seater National Stadium stadium wore a deserted look as policemen outnumbered the spectators in the first session of the Test -- the first in 14 months that Pakistan has participated in.
Pakistan's last Test was against India at Bangalore in