Also, the CFC defence held firm despite pressure mounted by the Pune team in the dying minutes. The team had missed crucial points in the last two home games against Kerala Blasters and Delhi Dynamos by conceding goals near the end.
The former ISL champion went to the top of the standings on 20 points with the win, their sixth of the season.
The winning goal came courtesy a good move by the dynamic Raphael Augusto, who came in as a substitute in the second half.
The introduction of Augusto did the trick for the home side. His immaculate through pass found Nelson on the right. The winger cut his man before firing his shot past the Pune 'keeper.
The second half too saw the two teams create chances but the marksmen were not able to find success and the goalkeepers rose to the challenge.
The first half saw the teams come up with some chances with the visitors seeming to have the better of the exchanges. It was the home side which had the best chance with a penalty, which wasn't converted.
Chennaiyin missed a golden chance to go into the lead in the 23rd minute when Rene Mihelic muffed a penalty.
Mihelic, who stepped up to take it, came up with a shot towards the right side of the 'keeper. Pune goalie Vishal Kaith anticipated it and dived to make a superb save.
Emiliano Alfaro looked in inspired form and created a few chances in the first half, but they didn't result in goals. Also, Chennaiyin goal Karamjit Singh did a good job in keeping the Pune strikers at bay.
The two sides, looking to win and go to the top of the standings, began in right earnest with an attacking mindset.
Both sides created a fair number of chances in the first but their finishing let them down.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)