The northeast outfit surged to a 3-0 lead at breather after T Lalnunpuia put the team ahead in the 18th minute.
Forward Lalnunuia scored again two minutes later while T Jackichand Singh netted in the 29th.
After play resumed in the second half, Vasco got their act together and scored off Jose Colaco in the 57th mintue.
Royal Wahindoh players regouped soon and attacked the rival citadel as Ennio D'silva converted a crosspiece on the 60th mintue.
Vasco's M Mascarenhes reduced the margin in the 87th minute.
The second half of the match was played amid heavy downpour.
Earlier, Kalighat Milan Sangha and Md. Sporting Club had qualified for the main draw of the tournament, commencing here from September 19.
