An attempt by the opposition to have Zuma declared unfit for office because of alleged graft that was deemed to be in conflict with the constitution was brushed aside and he was elected unopposed.
Zuma, who heads liberation leader Nelson Mandela's African National Congress (ANC), had seen his personal image battered by a scandal over the spending of some USD 23 million dollars (17 million euros) of state funds on his rural home.
But he was assured of a second term by the ANC-dominated parliament, which swept to power in elections earlier this month.
The expected formality of the re-election was disturbed only by new lawmakers from the Economic Freedom Fighters (EFF), who turned up at parliament in bright red overalls, red hardhats and Wellington boots.
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The EFF charges that the ANC has betrayed the trust of poor black South Africans since taking power at the end of apartheid 20 years ago.
The newly formed party, led by breakaway ANC youth league firebrand Julius Malema, won 25 seats in the 400-seat parliament in elections earlier this month.
But the sole challenge to Zuma's nomination came from the official opposition, the centrist Democratic Alliance, which did not put forward an alternative candidate once its objection had been rejected.
Before entering parliament, EFF lawmakers danced and sang revolutionary songs on the steps of the imposing building in central Cape Town as a light drizzle obscured the iconic Table Mountain in the background.
Members of parliament representing other parties wore traditional suits and frocks.