At stumps, Paunikar was unbeaten on 113 off 156 balls with the help of 18 fours and a six as Railways came up with an improved batting performance in their second essay after starting their innings trailing Punjab by 109 runs.
Paunikar was ably supported by his opening team-mate V Cheluvaraj (40 off 81 balls) as the two produced 108 runs for the opening stand.
Earlier, Punjab added just 84 runs to their overnight score of 230 for five before being bowled out for 314 in their first innings in reply to Railways' 205.
Punjab's overnight star batsman Uday Kaul could add just four runs to his yesterday's score to complete his century before Railways skipper Sanjay Bangar cut short his stay, caught by Anureet Singh.
Kaul faced 213 balls during his patient knock which was studded with 12 boundaries.
Another overnight batsman Bipul Sharma, however, provided some resistence and played an important 45-run knock which came off 76 balls and was laced with nine hits to the fence and one over it.
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For Railways, Hardik Rathod (3/75) and Krishnakant Upadhyay (3/86) shared six wickets between them while Bangar scalped two wickets for 36 runs.
Brief Scores:
Railways: 205 & 183 for two in 50 overs (Amit Paunikar 113, V Cheluvaraj 40; Bipul Sharma 1/25).
Punjab: 314 all out in 105.2 overs (Uday Kaul 100, Amitoze Singh 55, Bipul Sharma 45; Hardik Rathod 3/75, Krishnakant Upadhyay 3/86).