Pankaj finished with figures of 19-8-30-5, while his pace partner Rituraj Singh (3/33) took three wickets and Deepak Chahar (2/32) accounted for two at the Captain Roop Singh Stadium here.
The visitors are now just a run away from taking the first innings lead with seven wickets remaining.
Put in to bat by Rajasthan, only the top three Madhya Pradesh batsmen -- Satyam Choudhary (27), Jalaj Saxena (39) and Naman Ojha (21) -- could reach the double-digit mark.
In reply, Rajasthan opener Siddharth Saraf (48) and one-down batsman in skipper Hrishikesh Kanitkar (21) put on a solid 55 runs for the second wicket.
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At close of play, Robin Bist was batting on 11 and giving him company at the other end was Ashok Menaria on 17.
Brief scores:
Madhya Pradesh 1st innings: 115 all out in 50 overs (Jalaj Saxena 39, Satyam Choudhary 27; Pankaj Singh 5/30, Rituraj Singh 3/33).