Odafe Okolie's late goal gave the Goa team a 3-2 victory and took them to fourth place on the league table.
JCT's Sunil Chetri has been adjudged the best player of the 11th National Football League.
A last-minute goal by substitute Louis Martins guided Churchill Brothers to a 4-3 win over JCT in the NFL.
Odafe Onyeka Okolie's 78th minute goal earned Churchill Brothers a 1-1 draw.
Mohun Bagan held Durand Cup champions Churchill Brothers to 2-2 draw.
Second half goals gave Peerless a 2-0 victory in the Kolkata Super Division football league.
\n\nA goal in each half gave the Kolkata side a 2-0 victory in the National Football League.
Odafe Okolie scored twice from the penalty spot to guide Sporting Clube de Goa to their first win at home as they rallied to beat Mumbai FC 3-2 in the Hero I-League, in Margao, Goa, on Sunday.
Sporting Clube de Goa held a lacklustre East Bengal to a goalless draw in their penultimate I-League fixture at the Vidyasagar Krirangan, in Barasat on Friday.
Summary of I-League football matches played across India on Friday.
Mohun Bagan's winless streak stretched to four matches as Sporting Clube de Goa rode on a Boima Karpeh double for a 2-1 win in the I-League at the Yuba Bharati Krirangan in Kolkata on Saturday.
Seeking to defuse tension and promote harmony and cultural exchanges, the local administration in association with Sharda University recently hosted a football match between two teams, having members from both Indian and African students.
The two giants of Indian football, Mohun Bagan and East Bengal, are facing turbulent times. On the pitch, East Bengal finished a respectable third in the 2012-13 I-League season, while Mohun Bagan finished a disappointing tenth.
Bogged down by inefficient administration and unable to attract financing, the once legendary football clubs of Kolkata are fading into irrelevance.