However the Brazilian was later released on bail and flew out of the country today, early in the morning.
Chennaiyin beat FC Goa 3-2 in a high-octane final to win the second edition of Indian Super League.
Goa police had arrested Chennaiyin captain Elano yesterday night for assaulting Salgaoncar.
He was later bailed out by Additional Sessions Judge Vinscent Silva who also allowed him to leave the country.
"Elano left this morning by 5 am flight for his country," advocate Rajiv Gomes who represented marquee Brazilian player in the court told PTI. The winning captain was booked under 341 (wrongful restrain), 323 (causing hurt) and 504 (intentional insult to provoke breach of peace).
The trouble broke during the post-match celebrations when Elano allegedly assaulted Salgaoncar in presence of FC Goa team members and another co-owner Srinivas Dempo after Chennaiyin's victory.
Dempo told PTI last night that Elano who was making fun of the team was asked to leave but elbowed Salgaoncar before exiting the place.
Advocate Gomes said Salgaoncar refused to get himself medically checked though the complaint was of an assault.
"The complaint looks frivolous as Salgaocar did not get himself medically checked. This instance is going to be bad for image of FC Goa and also international players will fear to play in the state if such complaints are lodged against them," Gomes added.
In a close match, FC Goa lost to Chennaiyian team much to the dismay of thousands of supporters who had gathered at the stadium to support the home team.