On a day when 15 wickets fell, Rajasthan took a 97-run first-innings lead, and then pushed Baroda onto the back foot by reducing them to 112 for six in their second innings with Pankaj taking three wickets for 55 runs.
When the stumps were drawn for the day, Irfan Pathan was batting on 52 along with Gagandeep Singh (0) with Baroda ahead by 15 runs with just four second innings wickets in hand.
It was pacer Deepak Chahar who got the first wicket when he forced Saurabh Wakaskar (12) to edge to wicketkeeper Azim Akthar. Pankaj then got the better of Abhimanyu Chauhan (1) and Aditya Waghmode (0), the first-innings centurion.
Pankaj sent Baroda opener Dhiren Mistry's (21) off stump cartwheeling before Aniket Choudhary, the left-arm seamer, took a wicket off his first ball of the innings, getting Pinal Shah (5) caught behind.
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Baroda captain Yusuf Pathan, who was recovering from a fever, did not take the field for the second day. It is not yet known if he will bat tomorrow.
Baroda had started the day on a positive note, with left-arm pacer Gagandeep Singh recording career-best 7/109.
At one point, Rajasthan were 191 for 5, still 45 behind Baroda. Gagandeep took three more wickets, but not before Rajasthan had taken an important 97-run lead.
Baroda: 236 and 112 for 6 in 34 overs (Irfan Pathan 52 batting; Pankaj Singh 3/55)
Rajasthan: 333 all out in 104.4 overs (Vineet Saxena 66, Suryaprakash Suwalka 74; Gagandeep Singh 7/109).