The Confederation of African Football (CAF) said the Kenyan team refused to take coronavirus tests, before the match in the Comoros capital Moroni in November and only did so when Comoros football officials insisted.
Sunil Chhetri drew level with Lionel Messi in terms of international goals.
Chhetri equalled Argentina's Lionel Messi's tally of 64 international goals during the match.
India beat Kenya 2-0 to clinch Intercontinental Cup
India had outclassed Kenya 3-0 in the league game at the Mumbai Football Arena, which was skipper Chhetri's 100th appearance in national colours.
India had blanked Kenya 3-0 in the league game at the Mumbai Football Arena, which was skipper Chhetri's 100th appearance in national colours.
Kenya will clash against hosts India in the final on June 10.
Sunil Chhetri had earlier appealed on social media, urging fans to back the team.
Captain Sunil Chhetri scored a brace on his 100th international game as Indian football team thrashed Kenya 3-0 at the Mumbai Football Arena on Monday.