The Proteas are already 2-0 down in the five-match one-day series after being thrashed by 180 runs in Saturday's opener, before falling by 17 runs in a rain-ruined game yesterday.
South Africa have now lost 11 consecutive one-day matches on Sri Lankan soil since 1993, but AB de Villiers' tourists must win Friday's third match in Pallekele to stay afloat in the series.
Amla, who missed the first match due to a stiff neck, fell awkwardly while fielding near the boundary line on Tuesday and was rushed to hospital, where scans showed a strain to the left groin muscle. Team manager Mohammed Moosajee said Amla was being put through intensive treatment to ensure he is fit to play in the rest of the series.
"Injuries of this nature usually take three to seven days to recover. But he will receive intensive treatment and rehab in the coming days to give him the best possible chance of being ready for the rest of the series."
Amla's injury will further weaken the tourists, who are without three frontline players -- fast bowler Dale Steyn, all-rounder Jacques Kallis and former captain Graeme Smith -- for the tour.
The third and fourth matches will be held in Pallekele on Friday and Sunday, before the action returns to Colombo for the final game at the Premadasa stadium next Wednesday.
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