Opener Pathum Nissanka has led Sri Lanka's fightback against hosts South Africa as they closed the second day of the second Test on 3-242, trailing by 116 runs.

Nissanka was dropped when he was on 22 and went on to punish the South African bowlers on Friday, helping to blunt a hostile seam attack at St George's Park in reply to the home side's 358 all out which had featured a century for wicketkeeper Kyle Verreynne.

But Nissanka was out on 89 after dancing down the wicket to spinner Keshav Maharaj, getting bowled as he missed with a wild swipe.

He had featured in a 41-run opening partnership with Dimuth Karunaratne, who scored 20 before being undone by a rising delivery from Kagiso Rabada that forced an edge behind to Verreynne.

The 26-year-old had been dropped in the slips by David Bedingham after another unplayable delivery from Rabada took a healthy edge and used the reprieve to put on 109 for the second wicket with Dinesh Chandimal, who departed for 44 as Dane Paterson forced him to prod away from his body and offer Verreynne another catch.

Angelo Mathews (40) and Kamindu Mendes (30) were still there at stumps and will resume on Saturday with Sri Lanka looking to wipe the deficit on the third day and then build a lead on a good batting track.

South Africa were dismissed before lunch but not before Verreynne notched up a thrilling morning century as the home side's tail wagged in adding 89 to their overnight score of 7-269.

Verreynne was still one run shy of his 50 when South Africa lost their eighth wicket in the third over of the day but his partnerships with the last two batters - Rabada and Paterson - took him to an unlikely three figures, as he went from 48 to 105 not out.

Together with Rabada, he put on 56 for the ninth wicket, adding 23 to the total before Asitha Fernando took out his stumps.

Verreynne needed 19 for his third Test ton when No. 11 batsman Paterson came in and he bludgeoned the bowling to swiftly get to three figures. The pair added 33 off 17 balls for the last wicket with Paterson the last man to fall.

Lahiru Kumara, who celebrated his 100th Test wicket on Thursday, finished with the best bowling figures of 4-79.

Verreynne was the second South African batter to hit a century in the innings after Ryan Rickelton scored 101 on the opening day.

The Test is a must-win for both countries in their bid to reach next year's World Test Championship final at Lord's.

South Africa beat Sri Lanka by 233 runs in Durban last week to take the first of the two-Test series.