Sony Norde and Lalpekhlua put the hosts ahead inside 25 minutes before Brazilian Marcelo Fernandes pulled one back for Yangon before the interval at the Indira Gandhi Stadium.
Forward Fernandes then scored again to draw Yangon level 19 minutes after the restart only for Lalpekhlua's second of the night two minutes later to win the tie for the I-League side.
Mohun Bagan currently top the group G on nine points from three games, five ahead of both Yangon and Maziya Sports & Recreation after the side from the Maldives defeated Hong Kong's South China 2-1 in today's earlier Group G encounter.