Karunaratne and opening partner Kaushal Silva (27) provided a solid platform for Sri Lanka with a 63-run stand before Pakistan hit back with three wickets in quick succession.
Karunaratne fell seven runs short of a hundred in the first Test in Abu Dhabi where Sri Lanka won by 21 runs to take a 1-0 lead in the two-match series.
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Pakistan middle-order batsman Azhar Ali has been rested for the five-match ODI series against Sri Lanka beginning October 13 in UAE.
Considering the fact that he had walked off the field during the first day itself, it begs the question why Pakistan's team management did not take him for a scan immediately and allowed him to bowl with a shin injury on the second day.
Pakistan were 51 without loss in reply in the day-night Test. Sami Aslam was 30 not out, and Shan Masood on 15. Leg-spinner Yasir Shah is the pick of the bowlers with 3-120. He returned to the dressing room for treatment after bowling just three deliveries of his 17th over.
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All these individual pieces have combined to form a nightmare for Pakistan where the fast bowlers look far from effective, one spinner bowls 50 overs or more and part-timers bowl far too many overs. The ball took his inside edge, hit his thigh pad, and clattered into his stumps.
He arrived with the team for the second day and came on to bowl in the 11th over of the afternoon. He scored 196 runs by playing 405 balls. Sri Lankan skipper Chandimal said Pakistani batsmen struggle against Herath.
Amir has been ruled out of the ODI series against Sri Lanka due to a stress-related injury in the right shin. His first stint of five-fors in four consecutive Tests came in 1990, during a back-to-back home series against New Zealand and West Indies.
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Pakistan vs Sri Lanka 2nd Test in Dubai will be broadcasted live on PTV Sports for & Sony Pictures Network on both SD and HD channels. Six teams have tried beforehand, and six teams have failed, Sri Lanka also failed to perform.