Jamshedpur remain at the fifth spot in the 10-team table with 16 points from 12 matches.
Much of the hosts' victory can be attributed to a smart double substitution from their coach Ranko Popovic, who returned to the Pune dug-out for the first time after serving a four-match suspension.
With the match drifting out of Pune's hands, Popovic chose to make a double substitution at half time, bringing in Marko Stankovic for Jonatan Lucca and Sarthak Golui for Isaac Vanmalsawma.
The changes worked as Pune had more thrust going forward and they managed to draw level.
It was a howler from Pune goalkeeper Vishal Kaith that allowed Jamshedpur to surge ahead. Kaith had clashed with one of the Jamshedpur defenders and allowed Wellington a free aim at goal. Wellington took that chance and scored with the outside of his foot.
Pune struck back in the second session. The score drew level when Gurtej headed home a off corner from inside a crowded goalmouth.
They surged ahead when Alfaro -- who had missed an unbelievable sitter in the opening half -- made amends as he was on hand to turn home a beautiful ball by strike partner Marcelinho.
Marcelinho himself could have added his name to the scoresheet, but Jamshedpur goalkeeper Subrata Paul came to his side's rescue in a one-on-one situation with the man who won the golden boot last year.
Jamshedpur should have taken at least a point from this game, but lacked sharpness upfront. They created several chances and should gave scored an equaliser. But they could not as the final touch was found wanting.
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