The Indian midfielder grabbed his first goal of the tournament at just the right time to seal the title for the team backed by La Liga champions Atletico Madrid.
Kolkata had their goalkeeper Apoula Edel largely to thank for keeping them in a game in which Kerala created the much better chances.
Ishfaq Ahmed carved out the best chance of a tight first half, but Edel stood up to the task after the experienced striker had weaved through a set of Kolkata challenges.
Rafique was introduced in the 74th minute, though his primary tasks after coming on were in defence as Kolkata continued to dominate.
Michael Chopra hit a low shot that Edel saved, but the former Paris Saint-Germain man's best was yet to come as he somehow denied the Englishman from five yards after the striker had neatly jinked free in the area.
Edel's heroics were rewarded in dramatic circumstances as Rafique nodded a left-wing corner beyond Kerala player-manager David James at the near post to seal Atletico's title.