Chandimal was left out of the team to play the fourth ODI after a string of low scores on the South African tour and could even miss the final match on Friday as he seeks to put a poor tour behind him.
"It was a hard decision [to leave him out]," Tharanga said. "We chatted to him and he was okay to rest. He needs a few days away from cricket. We all know he is a very good cricketer. He will come back in the next tour. For a few days he needs to get away from cricket and get some rest."
In 12 international innings across all formats on this visit, Chandimal has scored 180 runs all told at an average of 16.36. His highest return has been 36 in the second ODI in Durban and he has endured six single-figure scores. But a break would not be the obvious choice for the vice-captain.
He sat out Sri Lanka's last tour, to Zimbabwe, as he recovered from a hand injury and, earlier in the series, coach Graham Ford had said he thought Chandimal came into this tour "slightly underdone". Ford believed Chandimal is not far off his best but that he needed game time to get there.
Now it seems he may have to wait until the T20s in Australia, with his replacement Sundan Weerakkody impressing with a half-century in his second ODI.
Weerakkody took Sri Lanka to the brink of victory at Newlands and earned special praise from Tharanga for making the most of the chance he got against a strong South African attack.
"This series was a very good opportunity for youngsters to learn the game and the way we played today, everyone learnt really good lessons," Tharanga said. "Sundan playing his second game - the way he batted is good for him and the team."
The same could be said for Tharanga himself. Although a veteran of the international game, who has played for more than a decade, he has gone almost four years without an ODI hundred and has only recently returned to opening the batting. Tharanga batted in the middle order in 2015 and 2016 but now, back at the top, he has fulfilled a life-long dream to score a century in South Africa.
"Opening has given me the chance to get some big scores," he said. "It's very different conditions. The South African attack always has very good fast bowlers. To get a hundred in South Africa, as a batsmen, gives me a lot of confidence."