The Barcelona forward produced a wonderful individual performance at Soccer City in Johannesburg as Luiz Felipe Scolari's men continued preparations for the FIFA World Cup on home soil with a superb display of attacking football.
South Africa were looking to make a statement after a disappointing World Cup qualifying campaign, but Gordon Igesund's charges were unable to cope with Brazil's masterclass.
The visitors led 2-0 at the break, first Oscar clipping past Ronwen Williams from Hulk's superb pass before Neymar added a second with a driven effort on 40 minutes.
South Africa responded with Bernard Parker's flash shot from the edge of the area that went wide of the far post before the hosts were dealt a further blow when centre-back Bongani Khumalo was taken off the pitch on a stretcher following a collision with Marcelo.
Shortly before the half-hour mark, Brazil wasted a great chance to make it 2-0. Neymar pounced on a misplaced pass in midfield and surged towards Williams, but the goalkeeper stood up well to deny the Barcelona forward's chipped finish.
The 22-year-old drove at the South Africa defence before feinting left and drilling under Williams' legs from the left of the box.
And it took just 22 second-half seconds for Neymar to grab his second of the game, when he latched on to Fred's flicked pass and finished with a superb lob over Williams.
South Africa replaced Parker with Ayanda Patosi shortly after the hour mark and he almost had an immediate impact with a close-range strike that forced Julio Cesar into a fine reaction save.
Fernandinho added further gloss to the scoreline with a fierce 30-yard effort that nestled in the top corner. And Neymar grabbed his third in the closing stages when he swept home Jo's knock down.
