Salgaocar, who were looking to finish sixth, started well and took the lead in the 15th minute through Gabriel Obatola.
Dempo retaliated and restored parity five minutes later through Ryuji Sueoka as both the teams went into the breather locked at 1-1.
The second half was fought evenly and the match was heading for a draw before Periera struck for Dempo in the 90th minute.
Nicolau Borges from the left sent a long pass to Ryuji Sueoka who in turn relayed the ball to Pereira, who scored to give Dempo the win after nine defeats in a row and end the season on a winning note.