In a dominating display by the visitors, Karma Tsewang gave Pune FC the lead in the 11th minute while Subhas Singh completed the tally in the 47th minute.
Just a minute after James Moga's header from a freekick went wide, Pune FC went one up when Karma converted another Moga header in a similar fashion.
The win came for Pune FC after two back-to-back losses against East Bengal and Churchill Brothers as they improved their position with nine points, while Pailan remained on eight points after five matches each.
It was an aggressive display by Pune FC who pressed hard from the start against the promising local youngsters who failed to get their acts together.
There were some shots from long range, but those were off target even as Pune FC missed one at the breather when Izumi Arata squandered an excellent move by Japanese recruit Daisuke Nishiguchi.
The miss at the stroke of half-time did not cost the Pune team much as they went ahead after the changeover when Moga once again got into the act with another fine header that Subash converted with a scorcher from the top of the box.
The local challengers came close to scoring in the 70th minute through Holicharan Narzary, but Pune goalkeeper Shahin Lal Meloly pulled off a brilliant save under the bar to keep their scoreline intact.
