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The Proteas chased down the modest target of 57 in just 8.5 overs.
Shanto blamed his batting unit for the disappointing run in the Super Eight stage of the T20 World Cup.
Former champions Australia were knocked out following Afghanistan's thrilling win over Bangladesh.
The 37-year-old opening batsman had always said the World Cup in the United States and Caribbean would be his farewell to international cricket.
The veteran all-rounder succeeded in his attempt to halt the play and the umpires took the players off the field with the arrival of rain.
Afghanistan hopes were dented when they were restricted to a modest 115/5 as showers around the ground threatened to change the calculations, but skipper Rashid Khan took 4/23 and Naveen-ul-Haq 4/26 in a defiant bowling effort.
Afghanistan kept their semifinal hopes alive with a well-earned 21-run win against Australia, and it will certainly heal the scars of the loss to the Aussies in last year's ODI World Cup.
India sit pretty with with two wins from as many games.
Their maiden win over Australia will instill greater belief in the minds of Rashid Khan & Co.
Half-centuries from Gurbaz and Zadran helped the Afghans rack up 148/6 in their 20 overs, before their bowlers dismissed the Australians for 127 on a tricky Kingstown track.