As South Africa awaited a final security assessment on whether it was safe to play in bomb-hit Colombo, organisers had hoped for a prompt start to the day-night international on Wednesday.
But heavy overnight rain and another sharp shower on Wednesday morning waterlogged the Premadasa stadium and left ground staff struggling to dry the slushy outfield despite a brief spell of sunshine.
Match referee Chris Broad of England abandoned the match at 3:15 pm (0945 GMT) as conditions did not improve. The game will now be played on Thursday, weather permitting.
The original series opener between South Africa and Sri Lanka was rained off on Monday and cancelled again on Tuesday following South Africa's reluctance to play amid security fears.
South Africa indicated they wanted to return home following a blast close to their team hotel here on Monday which killed seven people and injured eight.
The Proteas, however, agreed to extend their stay in Colombo pending an independent security assessment by the International Cricket Council which was expected to be announced later on Wednesday.
According to the revised schedule, the abandoned Sri Lanka-South Africa game will be played on August 29, the day of the final, which has now been put off until September 2.
South Africa's first match, if they take part in the series, will be against India on Saturday.
Each team is due to play the other twice in the league before the final. A reserve day has been kept aside for all matches in case of rain.