Teenager Manisha and M Nandhini scored for Sethu FC, which is the only team from Tamil Nadu participating in the premier competition being organised by the All India Football Federation.
The Group topper will qualify for the main draw.
Sethu FC had opened their campaign in the five-team all-play-all Group with a 16-0 rout of Baroda Football Academy last week.
R Sumithra scored in the opening minute but the goal was declared off-side.
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Sethu FC breached the rival defence for their second goal in the 79th minute, set up beautifully by Velanie Fernandes and Laura Estibeiro from the mid-field with the finishing touches provided by Nandhini, who came on as substitute for Sumithra.
The margin would have been bigger today had the side not wasted several scoring opportunities, especially in the first half.
Captain Rutuja Gunwant was elated about the win. "We have been working hard for the past three months," she said.