Their first innings ended on 372 all out, an overall lead of 168, with Michael Richardson ending on 96 not out and Brett Hutton taking career-best figures of five for 77.
The opening passage of the session produced a flurry of runs as Durham looked to prosper before the second new ball became due.
Chris Read turned to Hutton to arrest the momentum and the seamer struck twice, having Ryan Pringle caught at slip for 19, before bowling Jamie Harrison for nought.
Barry McCarthy was bowled by Luke Wood for just two and Chris Rushworth also nicked Hutton to Wessels for nine.
Richardson was on 92 when Graham Onions arrived in the middle but he could only add four more before losing the strike and Hutton quickly polished off the innings as the number eleven nicked through to Chris Read.
Notts had reached 30 without loss at tea, in their second innings.