Manuel Lanzarote (64') scored first but Anirudh Thapa (71') equalised seven minutes later to hand Chennaiyin an away goal.
Sergio Lobera made two forced changes for the home side. Laxmikant Kattimani replaced suspended Naveen Kumar in goal while Edu Bedia was fielded in an attacking role instead of the injured Hugo Boumous.
Bar Bikramji Singh, all other ten men on the field for Chennaiyin FC did not start in their last league game against Mumbai City FC.
Against the run of play, Chennaiyin FC had the first real chance of the match. Francis' low cross from the right wing in the eighth minute was latched on to by Jeje at the near post and his shot on the turn missed the far post by a few inches.
Mandar Rao Dessai looked lively on the left, but his deliveries left a lot to be desired. FC Goa missed a glorious chance in the 12th minute when Lanzarote entered the box and rounded Karanjit. But his chipped pass to Corominas was intercepted by an alert Mailson Alves.
Corominas then saw a shot blocked by Henrique Sereno. Soon after, Mandar's attempt from distance saw Chennaiyin goalkeeper Karanjit uncharacteristically fumble in front of the goal. But it thankfully went for a corner.
Nelson then managed to cut into the box from the left just before half-time but his subsequent shot just missed the far-post as the scores remained level at the break.
Chennaiyin FC started the second half with intent and forced Laxmikant Kattimani into a couple of saves from Jeje and Nelson in quick succession. Jeje managed to go past Juste but his volley could not beat Kattimani who, minutes later, denied Nelson from a one-on-one situation.
FC Goa also created a chance of their own as Pronay Halder played Corominas through inside the box but Mailson was there on time to put him off.
Mandar then managed to get beyond Calderon in one of the rare instances and his ball into the box found Coro. The former Espanyol striker saw his attempt being deflected off Thapa. Lanzarote was around to slam the ball home as he sent the assembled fans into raptures.
Just seven minutes after having taken the lead, Goa allowed Chennai to score the vital equalizer. Gregory Nelson eased past at least three players and found Thapa in space whose right-footed effort went through the legs of Chinglensana Singh and Kattimani to make it 1-1.
Both coaches threw in a fresh pair of legs in Brandon Fernandes and Mark Sifneos for Goa while Jaime Gavilan was introduced for Chennaiyin. Gavilan made an impact as he made his way into the box but his cross was intercepted by an alter Juste.
Sereno and Mailson went into the book after the former fouled Sifneos from behind. However, Edu Bedia’s curling free-kick was just about kept out by the visitors as they held on.