The storm had already claimed the lives of at least two people in China's Hainan and 16 people in the Philippines
Alastair Cook was 71 not out, including six boundaries, and Jonathan Trott remained unbeaten on 49 as the two batsmen shared a century stand.
Heavy rain delayed the start of play with the morning session wiped out and the teams taking an early lunch.
England finally resumed the day on 47-1, in reply to Sri Lanka’s first innings total of 400.
Ajantha Mendis (1-14) was the only Sri Lanka bowler to take a wicket at Sophia Gardens, removing nightwatchman James Anderson for 1.
Anderson can bat but won’t bowl for the rest of the test after incurring a grade one side strain during play on Friday where he ended with 3-66.
Before England had added to its overnight score Anderson fell to the 17th ball of the day, caught by Mahela Jayawardene in the slips.
But batting conditions improved and, after a tentative start, Cook and Trott went on the attack.
Cook reached 50 from 112 balls, while Trott was helped when he made his ground before a direct hit from Suranga Lakmal hit his stumps and rebounded to the boundary for four overthrows.
The century partnership was brought up when Cook glanced the final ball of the afternoon session from Mendis to deep midwicket.
The storm had already claimed the lives of at least two people in China's Hainan and 16 people in the Philippines
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