South Africa, who played a disciplined game, scored through Lyle Foster(21st minute), Mswati Mavuso (54th) and Luke le Roux (82nd).
Russia, who enjoyed territorial advantage, created several chances but could not get past rival custodian Glen Baadjie. However, Russia pulled one back through Skrobotov IIia in the 45th minute.
South Africa, who finished second with seven points from four matches, will face Brazil in the final on Saturday.
Russia, meanwhile, finished third with six points from as many matches.
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South Africa came with a counter move and took the lead in the 21st minute through Lyle Foster.
Russia, who went into offensive in search of the equaliser, came close with Kolesnichenko Kirill and Lopatin combining well upfront.
However, Russia drew level in the dying minute of the first half from a corner with Skrobotov IIia deflecting the ball into the net as Glen was beaten by the flight of the ball.
Unpreturbed by the set back, Russia kept on mounting pressure on their rival and had two clear chances but first Klesnicheako Kirill's left footer was put out by keeper Baadjie and few minutes latter Kirill and Daniil failed to put the ball into the net off a cross from the right after the South Africa defence was beaten.
South Africa came up with a counter move and sealed the victory with another goal in the 82nd minute.
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