Mohammad Hafeez was unbeaten on 31 and Younis Khan, playing his 100th Test, was on two after surviving an appeal for leg-before on zero.
Prasad, who took the field despite having suffered a finger injury during net practice on Wednesday, struck with the first ball of his second over to make it 5 for 1 at the P. Sara Oval.
Prasad forced Ahmed Shehzad to edge a rising ball to second slip where the 37-year-old Kumar Sangakkara dived to his right to pick up a low catch.
Another review by Sri Lanka in the next over for a leg-before appeal by Angelo Mathews against Khan was turned down. The on-field umpire's decision stood as replays showed not enough of the ball hitting the top of off-stump to overturn it.
Pakistan, who won the toss and elected to bat on the hard, bouncy pitch, retained the same side that won the first Test in Galle by 10 wickets to take the lead in the three-match series.
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