Sachin Baby's fine hundred went in vain.
The Panthers won by 1-run against Sachin Baby's Lions.
Kerala as bowled out for 178 in the second innings after conceding a lead of 140 runs.
Sijomon Joseph, Rohan Prem and Vinoop Manoharan are the other senior players in the 15-member squad.
Kerala (21 points) missed out to Jharkhand (23) for the second qualifying spot behind group-toppers Karnataka (35).
Pondicherry ended the third day on 34/1 in their second innings, an overall lead of 119.
However, the draw was enough for Karnataka to seal their place in the quarterfinals.
Sachin's 10th first-class hundred lifted Kerala to 224/6 at stumps on the opening day against Karnataka.
Sachin, who notched up his ninth first-class ton, also went past the 4,000-run mark during the course of the day.
Facing a daunting target of 395 for a win, Kerala finished their second innings at 299 for 8 wickets.