Chatterjee scored 107 and shared a 152-run stand for the fourth wicket with former Kolkata Knight Riders batsman Yashpal Singh as the hosts finished their first essay at 335 in reply to Kerala's 314.
Chatterjee batted for nearly seven hours facing 313 balls hitting 14 boundaries in the process. The burly Yashpal was quicker of the two as he scored 89 off 147 balls with 16 hits to the fence.
Services resumed third day's play on 84 for 2 with Chatterjee on 27 and Soumya Swain (30). Howvever, Swain failed to add to his overnight score and was dismissed by right-arm pacer Perumparambath Anthaf.
The home team scored 335 runs in their reply thereby taking an important 21-run lead in the first innings.
For Kerala, Pacer Sandeep Warrier took four wickets for 86 runs. Spinner Rohan Prem and pacer Chovakkaran Shahid shared two wickets apiece.
Kerala, in their second innings, were nine for no loss when the stumps were drawn.
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Brief Scores: Kerala: 314 and 9/0 (Abhishek Hegde 8 not out)
Services: 335 all out in 119.1 overs (Soumik Chatterjee 107, Yashpal Singh 89; Sandeep Warrier 4/86).