Forwards Godfrey Silva (2nd minute) and Alvino Pereira (4th minute) put Salgaokar 2-0 up within the first four minutes before Pune FC pulled one back in the 68th minute through L Williams.
The second match of the same group between Sporting Club De Goa and Prayag United Sporting ended in 1-1 draw.
Pritam S Niwgthoujam opened the account for the Goan team in the 30th minute while Rajon Barman restored parity for Prayaf just a minute later.