Pathan blazed away to 60 off 29 balls to help KKR achieve the target of 186 with five balls to spare at the M Chinnaswamy Stadium.
Andre Russell made 39 off 24 balls in a brilliant match-turning fifth-wicket partnership of 96 runs in just 7.2 overs.
The Knight Riders were back to the second position in the points table, while RCB's hopes of qualifying for the playoffs took a beating.
Pathan smashed six boundaries and three sixes, while Russell cleared the fence four times. Joining force at a difficult situation, Pathan and Russell kept their side in the game till the Indian brought KKR within sniffing distance by hitting Shane Watson for 24 runs in the 17th over. Pathan then collected 16 runs off Tabraiz Shamsi in the 19th over.
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When Gambhir was walking back to the dugout after being trapped by a full-length delivery from Sreenath Aravind, KKR were struggling at 66 for three, and the situation got worse when Manish Pandey was dismissed by Watson three runs later.
KKR accumulated 16 runs in the next over bowled by Varun Aaron. Coming in to bowl the 17th over, Watson was smashed for four boundaries and a six to help KKR close in on the target.
(REOPENS REL 55)
Earlier, Royal Challengers Bangalore plundered 54 runs in last three overs to post a competitive total after skipper Virat Kohli (52) and KL Rahul (52) struck half centuries.
Binny smashed two sixes and a boundary in the last over while facing only four balls. Umesh Yadav, who was allowed to continue despite bowling two beamers, was hit for 20 runs in the last over and finished with expensive figures of 1/56 in four overs. Umesh gave away 23 runs in the 18th over, which turned things around for RCB.
Young Rahul smashed six boundaries and two sixes during his 32-ball knock, while Kohli found the fence four times while facing 44 balls at the M Chinnaswamy Stadium.
Royal Challengers Bangalore were dealt a blow as Chris Gayle, playing in his first game since returning from the West Indies after the birth of his daughter, gave away his wicket by going for an extravagant shot against Morne Morkel.
The South African pace ace got a bit of extra bounce that unsettled Gayle who mistimed a pull shot to give an easy catch to wicketkeeper Robin Uthappa. Just before getting out, Gayle hit Morkel straight down the ground for a six.
However, while trying to shift gears and accelerate the run rate, Rahul got out to Chawla in the 12th over with RCB at 92 for two.
A B de Villiers (4) failed to get going as he was trapped by Chawla. Kohli, who got a reprieve when Gambhir dropped a sitter off the bowling of Morkel, got out in the very next ball while trying to force the pace.
Morkel (2/28) and Chawla (2/32) were the most successful bowlers for KKR, while Narine (0/45 in 4 overs) was a bit expensive.