Double strike from Afghan defender Haroon Amiri (20th & 25th minute) put Dempo SC in the driver's seat before a late strike from India international Jeje Lalpekhlua (90th) ensured a comfortable three points for five-time champions.
The hosts played the second half with 10 men after defender Gurjinder Kumar was sent-off for a second booking in the 55th minute.
The loss meant Pune FC ended their I-League 2013-14 campaign in the seventh place with 29 points from 24 games, their lowest finish ever in the marquee event.
Pune FC dominated the opening quarter and created a couple of chances with playmaker Riga Mustapha going the closest from edge of box only to be denied by 'keeper Laxmikant Kattimani.
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Minutes later, Dhanpal Ganesh went close but his grounder on the run was blocked by the keeper after being set up by Mirjan.
Twenty minutes in, Amiri put the visitors 1-0 up heading home Holicharan Narzary's cross in from the right.
Five minutes later, Amiri doubled the lead while completing his brace. Timing his run to perfection, the Afghan international nudged home Clifford Miranda's free-kick in from the right flank from close range leaving Amrinder Singh helpless.
Moments later, Douhou went on a brilliant solo run carrying the ball from the Pune FC half and covering almost 40-yards. However, his attempt from 5-yards outside the box down the middle was wayward.