Pathan (72 off 44 balls) looked set to win it for Kolkata until he was given out for obstructing the field. His wicket proved to be the turning point as the hosts fell short of Pune's 170 for four by seven runs. Kolkata ended at 163 for seven.
With the loss, slim hopes of Kolkata making the play-off dashed while the fine win for Pune ended their 10-match losing streak.
Kolkata were going along nicely when Pathan and Ryan ten Doeschate (42 off 30) were in the middle. They needed 49 off the last 30 balls.
But the scenario changed with the dismissal of Doeschate and Manoj Tiwary in consecutive overs, making 128 for five in 16.2 overs.
The explosive Pathan was still there and it meant all was not lost for the defending champions.
In the end, Kolkata's fate was sealed in unusual circumstances. Pathan wanted to take a single which his partner Debabrata Das refused. Realising the ball was on the pitch, Pathan kicked it away from the bowler, leading to an appeal from Pune. The third umpire did not take much time in giving the decision in favour of the visiting team.
Kolkata needed 18 off the last over and Angelo Matthews conceded only 10. Pathan's effort went in vain but gave the crowd plenty to cheer about. He hammered eight fours and two sixes in his entertaining innings.
Earlier, Manish Pandey (66) guided Pune to a competitive total with other contributions coming from skipper Aaron Finch (48) and Yuvraj Singh (30).
Pune Warriors India
Robin Uthappa b Senanayake 25
Aaron Finch b Balaji 48
Manish Pandey run out (Bisla/Kallis) 66
Yuvraj Singh c ten Doeschate b Kallis 30
Luke Wright not out 0
Extras (w 1) 1
Total (Four wickets in 20 overs) 170
Fall of wickets: 1-41 (Uthappa, 5.4 overs), 2-97 (Finch, 12.5), 3-162 (Pandey, 19.3), 4-170 (Yuvraj Singh, 19.6 ov)
Lakshmipathy Balaji 4-0-41-1
Sachithra Senanayake 4-0-22-1
Sunil Narine 4-0-26-0
Jacques Kallis 4-0-48-1
Rajat Bhatia 3-0-26-0
Ryan ten Doeschate 1-0-7-0
Kolkata Knight Riders
Gautam Gambhir c Yuvraj Singh b Ishwar Pandey 12
Manvinder Bisla lbw b Parnell 1
Jacques Kallis b Parnell 1
Yusuf Pathan obstructing the field 72
Ryan ten Doeschate run out (Murtaza/Uthappa) 42
Manoj Tiwary c Manish Pandey b Kumar 0
Debabrata Das not out 8
Rajat Bhatia run out (Uthappa/Mathews) 10
Sachithra Senanayake not out 2
Extras (lb 4, w 11) 15
Total (seven wickets in 20 overs) 163
Fall of wickets: 1-17 (Bisla, 1.4 overs), 2-25 (Kallis, 3.6), 3-29 (Gambhir, 4.4), 4-127 (ten Doeschate, 15.5), 5-128 (Tiwary, 16.2), 6-148 (Pathan, 17.5), 7-160 (Bhatia, 19.4)
Bhuvneshwar Kumar 4-0-22-1
Wayne Parnell 4-0-34-2
Ishwar Pandey 2-0-17-1
Angelo Mathews 3-0-25-0
Ali Murtaza 4-0-34-0
Yuvraj Singh 1-0-11-0
Luke Wright 1-0-11-0
Raiphi Gomez 1-0-5-0
Toss: Kolkata Knight Riders chose to field
Umpires: N.J. Llong (England) and K. Srinath
TV umpire: V.A. Kulkarni
Match referee: R.S. Madugalle (Sri Lanka)
Reserve umpire: P.K. Khakhar