Harambee Stars lost 3-0 to hosts India in their second match of the inaugural Hero Intercontinental Cup match at Mumbai Football Arena on Monday.
After a goalless first half punctuated with heavy down pour rendering the pitch rather waterlogged, Indian captain Sunil Chhetri broke the deadlock in the 68th minute from a controversial penalty.
Chhetri, playing his 100th game for India, was adjudged to have been tripped by Michael Kibwage while through on goal with the referee pointing to the spot.
The 33-year-old converted past Patrick Matasi.
Matasi conceded the second goal two minutes later as Jeje Lalpekhlua fired in a pile driver sending the thousands of India fans into frenzy.
Chhetri returned to claim a brace in added time with a fine chip over Matasi.
Kenya, who beat New Zealand 2-1 in the first match played on Friday, next plays Chinese Taipei in their round robin game on Friday.
Kenya had an injury set back prior to kick off with coach Sebastian Migne forced to replace Erick Ouma with Bolton Omwenga after the former picked a knock in warm up.
Neither of the teams created chance in a dull first half.
Chhetri saw his 21st minute shot from distance go wide with Patrick Matasi off his line.
Three minutes later, Ovella Ochieng's shot was blocked by Anas Edathodika as the tempo slowed down towards the break with teams resorting to long balls.