But fast bowler Morne Morkel pulled up after bowling three overs with the recurrence of a groin injury and took no further part in the game.
Duminy shared successive stands of 49 for the second wicket with Alviro Petersen, 70 for the third with AB de Villiers and 82 for the fourth with Francois du Plessis to help South Africa to 271 for six in their 50 overs.
New Proteas coach Russell Domingo sees Duminy's future at number three position in the one-day side. The 29-year-old fell eight runs short of his century after facing 100 balls.
Morkel opened the bowling in the Board President's XI's innings but was forced to retire at the end of his third over in obvious discomfort.
South Africa's media manager Lerato Malekutu said Morkel had suffered a recurrence of a groin injury and stopped bowling as a precautionary measure.
"It is the same Grade 1 injury to his left quadriceps muscle he suffered during the Champions trophy in England," said Malekutu. "We didn't want to risk bowling him."
Morkel bowled 6.5 overs in the Champions Trophy match against India before leaving the field. He took no further part in the tournament.
In Colombo, the pitch was a slow seamer but the Proteas' non-pace trio of Duminy, Aaron Phangiso and Robyn Peterson took seven wickets between them. The impressive Chris Morris took the other three, for 27 runs, as the home side were dismissed for 198.
South Africa start their five-match one-day series against Sri Lanka in Colombo on Saturday. They also play three T20 internationals.
(Reporting by Nick Said; editing by Robert Woodward; nick.said@thomsonreuters.com +27832722948 Messaging nick.said.thomsonreuters.com@reuters.net; To sign up for our Global Sports Forum chatroom, click on https://forms.thomsonreuters.com/global_sports_forum)
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