At stumps on the penultimate day, Kerala were 306 for four with skipper Sachin Baby (54 batting) and Robert Fernandez (29 batting) at the crease.
Maharashtra had scored 314 in their first innings, thereby taking a 163-run lead over the hosts who were bowled out for 151 in their first innings.
Opener Nikhilesh Surendran top-scored for Kerala in their second essay with a fine 159-ball 83, while Sanju Samson made an equally impressive 66 off 136 balls at the Conor Vayal Stadium.
Brief Scores: Kerala 151 and 306 for 4 in 100 overs (Nikhilesh Surendran 83, Sanju Samson 66, Sachin Baby 54 batting; Chirag Khurana 2/81).
Maharashtra: 314 all out in 109.2 overs (Harshad Khadiwale 97, Akshay Darekar 52; V Manoharan 4/60).