Both the teams fought keenly as they tried to exert pressure but failed to break the deadlock in the first half until the visitors took the lead in the 83rd minute through Sahib Malik.
But the Goans regrouped and restored parity in the 88th minute through Aaron Barreto.
With the match poised to end in a draw, Chandigarh struck the winner in the injury time through Manvir Singh.
With both the teams qualified for the knockout stage from this group, Goa, who lost their first match, topped the group with nine points followed by Chandigarh.
West Bengal, who led 2-0 at half time, scored through Rahim Ali (14th, 85th), Arnab (40th), Tarak (49th) and Abhijit Mondal (56th). Bakit Nongrum pulled one back for Meghalaya in the 20th minute.
