Pathan cracked five sixes and three fours in his knock but it didn't prove enough as his team slumped to its third straight defeat in the competition.
Chasing 171, Punjab were set back early in their innings when Manvinder Bisla was run out for a duck, before captain Kumar Sangakkara was sent back by fellow Sri Lankan Chaminda Vaas for no score.
Opener Ravi Bopara kept Punjab in the hunt but kept losing wickets at the other end, with Yuvraj Singh falling for four before Mahela Jayawardene and Adrian Barath were sent back cheaply as well.
Vaas' opening spell broke the back of the Punjab batting in which he took two wickets while every other Deccan bowler picked up a wicket each. Andrew Symonds starred for the Chargers with both bat and ball. It was also the first instance that Deccan had beaten Punjab in the IPL in five meetings.
Earlier, the Chargers threw away a cracking start to post 170-7 as the IPL staged its first game at at the Barabati stadium.
Andrew Symonds was the top-scorer with 53 but Deccan failed to build on a perfect launch pad set up by captain Adam Gilchrist, who scored 33 from just 12 balls after Punjab captain Kumar Sangakkara won the toss and decided to bowl.
Gilchrist's wicket was followed by an unfortunate incident for the Chargers, who lost opener VVS Laxman to injury. The batsman got his by a wayward throw while trying to make his ground while taking a run.
Herschelle Gibbs and Symonds, however, kept the Chargers on track for a big total as they cruised to 100-1 at the halfway stage. But Yuvraj Singh's introduction undid their good work as Gibbs fell for 23, before Rohit Sharma was run out in the same over.
Deccan kept losing wickets in the second half as they only managed 70 runs in their next 10 overs.