Set an improbable target of 529 runs for an outright win, South Zone were bowled out for 234 in 71.2 overs.
South Zone trail by 375 runs with four wickets in hand and a full day's play remaining.
The opener remains unbeaten on 209 as West extended the lead to 319 at stumps on day three.
In response to West Zone's total of 270, South Zone were 318/7 at stumps on day two.
Kerala pacer Basil Thampi bagged two wickets for the South Zone while Het Patel remains unbeaten on 96.
The opener brought up his fourth first-class hundred in just his sixth innings since debut off 172 balls.
The two Kerala players are part of the 15-member squad that will be led by Hanuma Vihari.
The maestro feels Duleet Trophy can be reinvented by bringing in the Ranji Trophy semifinalists along with two teams of promising Under-19 and U-23 players.
The BCCI has demanded having qualified medical practitioners as Lead Dope Control Officers.
The selectors had picked Gupta in the Indian Red squad for Duleep Trophy. According to a revised statement by the BCCI, selectors were not even aware of Gupta's suspension.