Down by a third-minute goal scored by Nepal's Dipa Adhikari, Supriya Rout Roy restored parity for India five minutes later.
Both the teams were locked 1-1 at the interval.
Changing over, India doubled the score in the 64th minute through Bem Bem Devi.
Kamala Devi completed the rout in the 87th minute.
The All India Football Federation (AIFF) congratulated the team.
"The Women's team displayed exemplary character both on and off the field as they breezed past every obstacle on the way. I congratulate the players and support staff for the achievement," President Praful Patel said in a message.
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General secretary Kushal Das also had a word of praise for the winning squad.
"The AIFF left no stone unturned for the preparation of Women's Team and the results are in front of us. I congratulate the team for the success," Das said.
"Football in India is on the rise. AIFF's aim stays to popularise the sport among the women. I'm sure the result will go a long way in inspiring a new generation to take up the sport," he added.