The home side - who went into this encounter, their game in hand over leaders Yorkshire, in second place and 5.5 points off the summit - had managed to post only 245 for their first innings on day one.
But they had reduced their opponents to 60 for three by the close of play, and Onions, having claimed two wickets within that effort, added two more this morning, with third-placed Sussex struggling to get momentum into their reply.
Two wickets for Mitchell Claydon, taking him to three for the match, and three for Usman Arshad followed, before Durham got their second-innings to 14 for no loss by lunch.
At the other end of the table, basement boys Derbyshire established a first-innings lead of 195 over third-bottom Somerset at Taunton.
The away side, who bowled out their hosts for 103 on day one, moved from 220 for five overnight to 298 before being halted, with Richard Johnson having top-scored on 68.
Johnson was one of three victims of Alfonso Thomas, whose team went in for lunch on five without loss.
Second-bottom Surrey brought Middlesex's first innings to an end on 294 at the Kia Oval before recovering from the early dismissal of Arun Harinath to take their own to 59 for one at lunch.
Meanwhile, Nottinghamshire, having ended Tuesday on a poor 14 for three in response to champions Warwickshire's 298 at Trent Bridge, had built their way to 136 for five at the interval, with Samit Patel not out on 68.