Hours before the start of the first ODI against Bangladesh, two Sri Lanka players and one coach tested positive for Covid-19.
Udana picked Ravindra Jadeja as the best all-rounder in the limited-overs format.
A waist-high full toss from RCB bowler Isuru Udana went unpunished during their Saturday night clash against SRH which left batsman Kane Williamson perplexed.
Udana hurt his back while attempting to stop the ball at short third man. Udana immediately hobbled off the field and did not return to take the ball.
Joseph has played for the Patriots since 2016; Udana has international commitments.
The England cricketer was ruled out of the event due to workload management, said Cricket South Africa (CSA) in a media release.
Bangladesh made two changes with Rubel Hossain and Anamul Haque coming in for Mustafizur Rahman and Mosaddek Hossain in their bid for a consolation win.
Angelo Mathews chipped in with an unbeaten 52 as Sri Lanka reached 242-3 in 44.4 overs after restricting Bangladesh to 238-8 in 50 overs.
Mushfiqur and number eight Mehidy Hasan shared 84 runs, a seventh-wicket record for Bangladesh against Sri Lanka, to give the visitors' innings some respectability.
Malinga dismissed dangermen Jos Buttler and Joe Root among his victims in a devastating spell that ruined England's bid to chase down Sri Lanka's modest total of 232/9.