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Sri Lanka, resuming at 220-5, had progressed to 225-5 in 7.5 overs when heavy rain in the morning forced the teams to have early lunch.
Play was stopped for two hours and 43 minutes but when it resumed only 10 overs were possible with Sri Lanka losing Niroshan Dickwella for 33 before bad light accompanied by rain forced an early call-off at 3:30 pm (1030 GMT).
At the close Sri Lanka were 263-6 with Dhananjaya de Silva unbeaten on 72 and Dilruwan Perera not out on two.
The stop-start play left both teams frustrated as well as 2,000 fans who had come to watch the revival of Test cricket in Pakistan.
When play resumed after lunch Pakistan took the second new ball and with it lanky pacer Shaheen Shah Afridi removed Dickwella, caught at gully by Babar Azam.
Dickwella, who hit four boundaries, added 67 for the sixth wicket with de Silva, thwarting Pakistan's attempts for early wickets.
De Silva has so far hit 11 boundaries in his 131-ball stay.
Earlier, the brief period of play saw wicketkeeper Mohammad Rizwan claim a catch to dismiss de Silva off the bowling of 16-year-old Naseem Shah, but third umpire Richard Illingworth ruled the ball had bounced.
On the next ball de Silva completed his half-century with two runs off Naseem, who with 2-65 was the pick of Pakistan's bowlers.
The Test is the first in Pakistan since a militant attack on the Sri Lankan team bus killed eight people in March 2009, leading to the suspension of international cricket in the country as foreign teams refused to visit over security fears.
With improved security, Pakistan hosted Zimbabwe, a World XI, West Indies and Sri Lanka in the last four years, but only for limited over matches.
Sri Lanka only agreed to tour after completing a limited over tour (three one-day internationals and as many Twenty20s) in September-October this year under tight security arrangements.Scoreboard
Sri Lanka 1st innings
D. Karunaratne lbw b Shaheen 59
O. Fernando c Sohail b Naseem 40
K. Mendis c Rizwan b Shinwari 10
A. Mathews c Shafiq b Naseem 31
D. Chandimal b Abbas 2
D. de Silva not out 72
N. Dickwella c Azam b Shaheen 33
D. Perera not out 2
Extras: (b 5, lb 6, nb 3) 14
Total: (6 wkts; 86.3 overs) 263
Still to bat: V. Fernando, K. Rajitha, L. Kumara
Fall of wickets: 1-96, 2-109, 3-120, 4-127, 5-189, 6-256
Bowling: Abbas 24-9-56-1, Shaheen 19.3-7-47-2 (nb3), Shinwari 15-4-54-1, Naseem 22-4-75-2, Sohail 3-0-12-0, Masood 1-1-0-0, Shafiq 2-0-8-0
Pakistan: Shan Masood, Abid Ali, Azhar Ali, Babar Azam, Haris Sohail, Asad Shafiq, Mohammad Rizwan, Usman Shinwari, Mohammad Abbas, Naseem Shah, Shaheen Shah Afridi
Toss: Sri Lanka
Umpires: Richard Kettleborough (ENG) and Michael Gough (ENG)
TV umpire: Richard Illingworth (ENG)
Match referee: Andy Pycroft (ZIM)
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