Ekene (72nd, 88th) scored a brace, Yakubu (19th) and Francis Fernandes (65th) netted one goal apiece for the visitors while Elija Junior (4th) reduced the margin for Chirag.
With this victory, Salgaocar now have 34 points from 15 matches while Chirag remained at the 8th spot in the 16-team league.
Meanwhile, in a totally one-sided encounter, hosts Viva Kerala thumped Air India 7-1 in Kannur on Sunday.
PK Anilkumar (8th, 48th, 83rd), Felix (38th), Karma (78th and 89th) and NP Pradeep (90th) scored for Viva Kerala.
The consolation goal for the visitors was struck by Okorogeor Praise in the 75th minute.
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