The Nigerian forward fired up a strong header into the right side of an open net from the six-yard box after being set up by Robert Lalthlamuana in the 55th minute to notch the record figure in combined I-League and NFL.
Martins, who is also the leading I-League scorer with 15 goals to his tally, took off his jersey to celebrate the milestone only to be handed a warning.
East Bengal on the other hand moved past Pune FC to occupy fourth place in the table with 23 points from 14 outings.
East Bengal could have easily doubled the lead in the 87th minute by cutting open Salgaocar but missed back to back chances.
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Martins missed in front of an open net after being set up up by Cavin Lobo who later wasted another chance, sending a looping shot towards the far post.
The Goan started well and dominated possession in the first quarter but the local heavyweights came into their elements with Martins and Dudu Omagbemi showing perfect co-ordination.
Salgaocar also protested for a penalty but referee turned it down after Nicolau Colaco was apparently brought down by Mondal.