Ganadeep's 19th minute goal made all the difference as Minerva left the EMS Corporation Stadium here with all three points, while hosts Kerala were left empty-handed.
Odafa Okolie could have made his Hero I-League debut for the Kerala-based side merrier, had he found the back of the net with his first touch in the first minute of the game.
After making some positive move earlier in the match, Gokulam Kerala FC slowly slipped into the shell as the visitors started to dominate.
After the goal, the Punjab-based side continued to push harder to double the lead but they couldn't breach the Kerala FC defence anymore till the halfway mark.
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Gokulam FC debutant Balwinder couldn't match up to the pace generated by Chencho in the 33rd minute providing the midfielder with another opportunity to hurl further damage to the hosts but eventually, Daniel Addo averted the danger.
Minerva Punjab FC went into the changing room with a slender lead of 1-0 at the half-time.
They earned three consecutive corners after the hour-mark but what they could only make was force Rakshit Dagar to make a fingertip save to keep the scoreline unscathed.
Odafa Okolie showed his sublime touch in the 72nd minute when he unleashed an inch-perfect pass to Usman but before the youngster could make any damage, Dagar threw himself to snatch it from Ashik's feet.
Chencho once again came very close to scoring but Balwinder intercepted well to avert the danger in the 84th minute.
Following the win, Minerva Punjab FC unsettled Neroca FC from the second spot with 16 points from 7 matches whereas Gokulam Kerala FC dropped to the ninth spot with mere 4 points having played the same number of matches.
Meanwhile, Minerva Punjab FC are within the touching distance of the pole position as the leaders Kingfisher East Bengal, who have amassed 17 points so far have played one match more until now.