Baoringdao Bodo (57th minute) and Anirudh Thapa (66th) scored for the Punjab side while Albeit Karan Sawhney (77th) pulled one back for Mumbai.
The win came after Minerva Punjab held Churchill Brothers to a draw in a creditable performance on Wednesday.
Mumbai, on the other hand, slumped to their fifth loss on the trot. They had won their opening two matches before losing the next five.
Mumbai, banking on coach Santosh Kashyap's innovative 3-1-4-2 formation, were led by Densill Theobald. Minerva were was led by Kareem and opted a 4-3-3 formation.
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After a barren first half, the second session kicked off with more urgency and both teams were eager to break the deadlock.
Tackles came flying end to end as Arashpreet was booked for a challenge on Steven Dias.
Minerva managed to score their first goal after a deflected cross from Anirudh Thapa and Bodo was there at the right place at the right time.
The next one came in quick succession for the home team after Thapa scored a free-kick goal which landed at the net beating Kattimani at the far post.
With today's win, Minerva Punjab FC leapfrogged Chennai City FC to the ninth spot at the table with five points whereas Mumbai are at sixth spot with six points.
Disclaimer: No Business Standard Journalist was involved in creation of this content