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Chasing a target of 221, India were struggling at 93 for five before Pathan launched a savage assault against South African off-spinners Johan Botha and JP Duminy.
On a pitch where most batsmen found it difficult to play positive strokes, Pathan, making his first appearance in the series, struck 59 off 50 balls as India took a 2-1 lead in the five-match series.
Pathan and Suresh Raina (37) put on 75 for the sixth wicket, but both were out in quick succession to set up a tense finish.
Fast bowler Morne Morkel took three for 26 and fellow paceman Dale Steyn claimed two for 31, but could not stop India from getting home with ten balls to spare. Harbhajan Singh made a crucial 23 not out, including two sixes.
The match changed dramatically in the 28th over of the Indian innings when Pathan, on six, edged Botha for a four between wicketkeeper AB de Villiers and captain Graeme Smith at slip.
Pathan swept the next delivery and Lonwabo Tsotsobe, running in from the boundary to try to take a catch, misjudged the ball and it went for another four.
In the next over from Duminy, Pathan again swept in the air and Morkel also misjudged the ball in contemplating a catch, with another boundary the result.
Then Pathan struck three sixes off four balls from Botha, all sailing over deep mid-wicket.
On an untypical Newlands pitch, South Africa struggled to 220 all out with newcomer Francois 'Faf' du Plessis and JP Duminy putting on 110 as they rescued a floundering innings.
Du Plessis made 60 and Duminy 52 on a pitch of inconsistent pace and bounce.
The pair came together with their side in trouble at 90 for four in the 24th over.
They put on 110 off 129 balls before Du Plessis slipped as he went down the wicket to attack Munaf Patel and sliced a catch to cover.
Du Plessis, 26, a former schoolboy team-mate of de Villiers who has been signed to play for Chennai Super Kings in the Indian Premier League, made his runs off 78 balls.
He showed composure at the crease, and the only sign of nerves came when he needed treatment for cramps in his forearm.
Du Plessis was out in the first over of the batting powerplay, which was taken in the 45th over, and as in the second international in Johannesburg, the lifting of fielding restrictions heralded a flurry of wickets.
Duminy was bowled in the next over and the innings folded rapidly, the last six wickets falling for 20 runs.
Zaheer Khan, with three for 43, and Singh led a superb Indian bowling performance, which was backed up by good fielding.
Khan repeatedly beat South African captain Graeme Smith with swing and movement off the pitch, although Smith survived to make a laboured 43 off 79 balls before falling to Harbhajan's off-spin.
Khan also took a spectacular diving catch in the outfield to dismiss De Villiers.
Harbhajan mesmerised the batsmen, taking two for 23 in nine overs, helped by two diving slip catches by Virat Kohli.
