The 38-year-old Ganguly remained unbeaten on 32 off as many balls as Pune, after being asked to bowl first, achieved the target with 10 balls to spare.
After Mitchell Marsh helped Warriors restrict the hosts to 136 for eight with impressive figures of four for 25, Manish Pandey was unlucky to miss a well-deserved half century by a run but did enough to pave the way for his team's victory.
Equally impressive was Pandey's opening partner Jesse Ryder, who made a hurricane 35 of 20 deliveries.
But it was Ganguly who stole the limelight with a fluent unbeaten knock which contained three boundaries and a six.
In a match that generated interest as well as anticipation for the former India skipper's return to the highly popular tournament, Ganguly strode to the crease at the fall of opener Ryder's wicket.
In the company of Pandey who was just two years old when Ganguly made his international debut way back in the Australian summer of 1991, the experienced left-hander proved a point or two to all those who ignored him during the IPL auction in January.
A run-a-ball innings after a long lay-off was par for the course.
That he made those runs with the help of three boundaries and a massive six off Mishra over deep square-leg, only goes on to show that he still has it in him to play in the league.
Chasing a modest 137 for their fourth victory in the tournament, Pune rode on Ryder's enterprise and Pandey's controlled aggression to race to fifty in just six overs.
Slow left-arm spinner Pragyan Ojha broke the opening partnership by having Ryder bowled, but not before the burly New Zealander smashed five boundaries and two sixes.
Even as all eyes were on Ganguly, Pandey managed to play an innings which was as important as the one played by Ryder.
Boundaries came in thick and fast and there was no stopping the duo till Ryder went for that wild heave.
Skipper Yuvraj Singh and Robin Uthappa didn't last long enough as they were snared by Daniel Christian, but that hardly mattered.
Earlier, Marsh bowled with purpose after Deccan skipper Kumar Sangakkara elected to bat.
The Warriors did not get off to a good start as Chargers openers Shikhar Dhawan and DB Ravi Teja raised a half-century stand in six overs to set the tone for a competitive total.
But clever bowling coupled with some mindless batting helped the Warriors fight back into the match.
Besides Marsh, Yuvraj picked up two wickets including that of Dhawan, the team's first breakthrough.
Marsh and the other bowlers' efforts ensured that Dhawan and Ravi Teja's brisk start is wasted.
Bhuvneshwar Kumar bowled a tight first over conceding just four runs but, in the following over, Ravi Teja cut and drove Shrikant Wagh for two successive boundaries to make it run-a-ball.
Always on the lookout for opportunities, Ravi Teja then smashed Kumar for a four, before Dhawan got into the act with a powerful cut over point against Wayne Parnell.
Parnell was finding it difficult in the middle as Ravi Teja drove him on the up between mid-off and extra cover, to help the hosts inch towards the 50-run mark.
At the other end, Dhawan cleared the ropes at the Rajiv Gandhi International stadium twice to boost the scoring.
The Delhi boy danced down the track to loft Kumar over his head and then pulled Parnell's short delivery over deep square leg for another six.
The 50 was up by the seventh but Yuvraj Singh didn't let the partnership to flourish further, by removing Dhawan, who miscued a shot to give Jesse Ryder a simple catch at extra cover.
Ravi Teja, too, followed suit as he dragged one from Marsh onto his stumps.
Skipper Sangakkara didn't last long, falling prey to the guile of Rahul Sharma.
The leg-spinner has been very impressive in this edition of the league, and getting a quality player like Sangakkara only re-affirmed the belief that he is one for the future.
Daniel Christian was snapped up by Yuvraj, while Marsh came back to take the important wicket of Jean-Paul Duminy, who made 30 off 30 balls.
Bharat Chipli tried his bit, scoring a couple of boundaries, but that was not enough to take Chargers towards the 150 mark.
Scoreboard
Deccan Chargers
Shikhar Dhawan c Ryder b Yuvraj Singh 24
DB Ravi Teja b Marsh 30
Kumar Sangakkara lbw b Sharma 12
JP Duminy c Sharma b Marsh 30
Daniel Christian lbw b Yuvraj Singh 10
Bharat Chipli not out 18
Sunny Sohal c Uthappa b Marsh 0
Amit Mishra c Kumar b Marsh 0
Dale Steyn c Ferguson b Parnell 11
Ishant Sharma not out 0
Extras: (W-1) 1
Total: (For 8 wickets in 20 overs) 136
Fall of wickets: 1-51, 2-56, 3-76, 4-98, 5-119, 6-124, 7-124, 8-135.
Bowling: Bhuvneshwar Kumar 3-0-24-0, Shrikant Wagh 1-0-8-0, Wayne Parnell 4-0-38-1, Rahul Sharma 4-0-24-1, Yuvraj Singh 4-0-17-2, Mitchell Marsh 4-0-25-4.
Pune Warriors
Jesse Ryder b Ojha 35
Manish Pandey lbw b Mishra 49
Sourav Ganguly not out 32
Robin Uthappa c Sangakkara b Christian 1
Yuvraj Singh b Christian 2
Callum Ferguson not out 15
Extras: (W-2, NB-1) 3
Total: (For four wkts, 18.2 overs) 137
Fall of wickets: 1-55, 2-93, 3-96, 4-119.
Bowling: Dale Steyn 4-0-30-0, Ishant Sharma 3-0-25-0, Pragyan Ojha 3-0-13-1, JP Duminy 2-0-22-0, Daniel Christian 3-0-21-2, Amit Mishra 3.2-0-26-1.
