The game was heading for a goalless draw till the 88th minute when striker Goossens scored the goal with a header off a rebound from MacPherlin Dudu Omagbemi, whose powerful shot was stopped half-heartedly by United goalkeeper TP Rehenesh.
Throughout the match, both teams created several chances but their finishing was found wanting.
Both teams started positively but it was United who threatened early. Dong Hyun Do made a pleasing run into the box and his powerful blow was deflected to safety by Pune custodian Anupam Sarkar.
Greek veteran Konstantinos Katsouranis came close to score one but he chipped it just over the goal, much to the relief of the United fans. Katsouranis later made a smart cross from the left for skipper David Trezeguet, who reacted slowly.
For Pune, midfielder Israil Gurung created two best of opportunities in the 13th and 64th minutes but only to be averted by an alert Rehenesh.
First, he came up with a fine strike from outside the box but it was palmed away by the goalkeeper and then 50 minutes later, supplied a perfect cross inside the box for Goossens but it was quickly intercepted by Joan Capdevila, who was stationed quite close to the goal.
Gurung continued to work harder and later he passed it to Omagbemi, whose rebound shot found the head of Goossens and went inside the goal.
With this win, Pune moved to fourth position while United remained third in the standings.