Uthappa was unbeaten on 67 while Pawan scored 56 as the two batsmen shared a 112-run stand for the first wicket.
Left-arm medium pacer Gagandeep Singh took both the Karnataka wickets as he caught and bowled Pawan and then trapped Ganesh Satish (5).
Manish Pandey (10) was giving company to Uthappa when stumps were drawn for the day.
Earlier, Stuart Binny (5/65) took a five-wicket haul even as Baroda added 98 runs to their overnight total before their first innings ended at 406.
The hosts lost the two overnight centurions early as Binny scalped both Aditya Waghmode (129) and Irfan Pathan (121). Waghmode added just 8 runs to his overnight total while Pathan added 15 runs.
Pinal Shah (19) and Ketan Panchal (29) added some useful runs to take the side past 400-run mark.
Binny trapped Panchal to complete his five-wicket haul while KP Apanna (3/53) added the wickets of Shah and Gagandeep Singh to his kitty.
Brief Scores:
Baroda 1st innings: 406 all out in 123.4 overs. (Waghmode 129, Pathan 121; S binny 5/65, Apanna 3/53)
Karnataka 1st innings: 148 for 2 in 55 overs.(Uthappa 67 batting, Pawan 56; Gagandeep Singh 2/15).
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