High on confidence after beating Shillong Lajong FC 5-1, the Sukhwinder Singh-coached JCT scored the goals through Baljit Sahni (56th) and Penn Ikechuwu Orji (46th) who was awarded the Man-of-the-Match.
With three points from the match, JCT now have six points, while Bagan are yet to open their account after two matches.
In a match that once again saw Mohun Bagan reduced to 10 players after stopper Deepak Mondal was awarded two yellow cards, Bagan's only goal came through Branco Cardozo (84th) who replaced an injured Jose Ramirez Barreto.
In the 10 minutes stoppage time, Bagan players including Deepak were involved in an ugly incident that saw them go wild against the match officials after the defender was given a second yellow by referee A Rowan.
In total, the match saw a total of six single yellow cards besides two double yellow to Deepak resulting in a red card.
Orji Ikechuwu Penn gave JCT the lead in the 46th minute in what appeared a defensive blunder.
At first attempt, a JCT striker missed the cross by Balwant Singh from the right. Bagan's Mashangva Zenith cleared the cross but it was found by Penn in a perfect position in front of the goalmouth.
"It was a disappointing as our boys failed to penetrate into the rival's goal after controlling a major part of the match, which has led to our defeat. We need to learn from this," Sporting Clube de Goa coach Roy Barreto said. Meanwhile, Lajong coach Stanley Rozario attributed the victory to his players playing to a plan.
"We played to a plan adopting a defensive game and attack on counter. I am happy that our boys struck to the plan and succeeded in keeping our rivals at bay and defended till the end the first half lead," he said.
The first match was disappointing and I am happy that we bounced back from the disappointing loss against JCT. The victory has raised the morale of the team and will help the boys to play better against Dempo when we meet them next," he added. Rozario.