Bavuma and fellow batsmen Aiden Markram, Quinton de Kock and Rassie van der Dussen and fast bowlers Kagiso Rabada and Anrich Nortje were all rested.
Finishing third in a three-way tie on points might feel harsh, but on the evidence of the last few weeks it is what South Africa deserve.
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Markram batted in six innings for Punjab Kings in this year's IPL with a best score of 42. One of his innings stretched into the 17th over and two into the 16th in the IPL, something he might experience in the T20 showpiece even though he bats at the top of the order.
Shamsi and Markram took three wickets each to help bowl out Sri Lanka for 103, a total the tourists chased down in 14.1 overs to take an unbeatable 2-0 lead in the three-match series in Colombo.
Sri Lanka vs South Africa: Aiden Markram sets up 28-run win as Proteas go 1-0 up in T20I leg of tour
Markram's 33-ball knock guided South Africa to 163-5, a total they defended by restricting Sri Lanka to 135-6 to lead the three-match series 1-0 in Colombo.
South Africa fell short on 286-6 despite opener Aiden Markram's 96 off 90 balls and a run-a-ball 59 by Rassie van der Dussen.
The first of three T20s wasn't competitive, surprisingly so after a thrilling one-day international series that was drawn 1-1 last week.
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West Indies skipper Kieron Pollard slammed his players for not learning from their past mistakes.
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Set a target of 168 after captain Kieron Pollard belted an unbeaten 51 off 25 balls with five sixes and two fours to lift the West Indies to 167 for six, the Proteas relied heavily on the consistent Quinton de Kock in their quest to clinch the contest ahead of the final match on Saturday at the same venue.
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Ngidi’s haul of five for 19 was his second five-wicket innings haul in Test cricket, the bulk of his success coming in the afternoon session after seamer Anrich Nortje pushed the West Indies on the back foot with three of the four wickets to fall in the pre-lunch period.
Anrich Nortje, Aiden Markram among names nominated for top CSA awards; Shabnim Ismail included in women’s lists
Besides Markram and Nortje, South Africa's limited-overs captain Temba Bavuma and top-order batsman batsman Rassie van der Dussen have been nominated in the Men's Player of the Year category.
South Africa vs Pakistan: Aiden Markram, Heinrich Klaasen score half-centuries as hosts win second T20I to level series
Markram hit 51 off 32 balls and Klaasen scored 50 off 28 deliveries as a depleted South African team made 188 for six off 20 overs after winning the toss.
South Africa vs Pakistan: Mohammad Rizwan's 74 not out helps visitors pull off record chase, gain T20I series lead
Rizwan made an unbeaten 74 as Pakistan chased down a target of 189 with one ball to spare. Their previous highest T20 chase was 188 against Australia in Harare in 2018.
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Hasan finished with 5-60 to record his best match figures of 11-114 and help dismiss South Africa — who were set a daunting 370 to chase — for 274 before the tea break.