James Moga scored the all-important goal in the added time of the first half. The South Sudanese striker volleyed home after being fed by Douhou Pierre who cut past two defenders to thread the pass.
Pune FC are now in third spot in the league standings with 40 points from 22 matches.
This was ONGC's first loss in their own den since Santosh Kashyap took over the reins last year in November. It leaves them to ninth spot with 30 points from 24 matches.
The visitors had the better of the exchanges from then on with Izumi Arata playing the role of a schemer to perfection. The India International was all around the park creating goalmouth chances aplenty for Moga and Douhou Pierre. One such move saw Pierre in the clear but his shot sailed over the bar.
ONGC were uncharacteristically off colour at home. Their key player Japanese playmaker Yusa Katsumi failed to find his feet and his colleagues up front lacked purpose too.