The loss was DSK Shivajians' first in the competition, while Minerva FC registered their first win.
The match was goalless during the first-half. DSK Shivajians were first to score when Spaniard Juan Quero converted a penalty-kick in the 60th minute.
Minerva FC equalised through Lago Bei (79th minute), before Manandeep Singh (90th minute) won it for the Chandigarh-based team.
DSK Shivajians chances of making it to the semi-finals took a beating with the loss and now they must win in their last match against Army Green on Monday.
DSK Shivajians (seven points from four games) lead Group A, followed by Indian Navy (six from four). Close behind are Army Green (five from three).
Sporting Clube de Goa (four from four) and Minerva FC (four from four) share the fourth spot, while Gangtok Himalayan (three from three) are at the bottom.
