Jayawardene ended on 240 and Samaraweera struck a career-best 231 as the tourists declared their first innings at 644-7, their best ever total against Pakistan, on the second day at the National Stadium.
Pakistan, who must score 445 to avoid the follow-on in their first Test in 14 months, were 44-1 at stumps with debutant Khurram Manzoor on 18 and Younus Khan yet to score.
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With the twin threats of Ajantha Mendis and Muttiah Muralitharan, the world record-holder for Test wickets, looming large on a pitch likely to take spin, Pakistan's task looks daunting.
"We need to bat sensibly," said Pakistan coach Intikhab Alam, who replaced Australian Geoff Lawson in October last year.
"The Sri Lankans batted well on a lifeless pitch and we bowled poorly on the first day.
I am not happy with the pitch."
Muralitharan gave signs of what is in store when he dismissed opener Salman Butt for 23 in the penultimate over to underline a dominant day for the tourists.
Skipper Jayawarde