Onions, on his 33rd birthday, claimed figures of five for 56 as the home side were skittled out for just 204, in only 54 overs, after being put in by Paul Collingwood. Notts had been reduced to seven for three early on but fought back to collect a batting point through half centuries from Luke Wood and Steven Mullaney.
Durham began their reply after tea and raced their way to 174 for two when bad light stopped play with 3.5 overs remaining, with Borthwick on 56 not out and Collingwood on 16.
Earlier, Stoneman had been dismissed for 62 and 18-year old Jack Burnham had fallen for 31.
Onions removed both Brendan Taylor and Michael Lumb during the early exchanges, after the home side had also lost Jake Libby to Chris Rushworth’s fourth ball of the morning.
Rushworth finished with two for 15 from 16 testing overs and he also removed Samit Patel to claim his 82nd Championship wicket of the season, beating Otis Gibson’s record for the county.
With John Hastings called away to bolster the Australian ODI squad, the visitors included Barry McCarthy for his Championship debut and the 22-year old right-arm seamer picked up the wicket of Riki Wessels before lunch, one of four catches to wicketkeeper Michael Richardson.
When Brett Hutton fell in the first over after lunch, the hosts’ found themselves on 73 for seven but Mullaney and Wood fought back with a positive stand of 92.
McCarthy blotted his copybook somewhat when he dropped Mullaney on the deep midwicket boundary but he regained his stripes by removing the same batsman for 63.
Wood passed fifty for the third time this season but was left high and dry on 65 as Onions bowled Jake Ball and Harry Gurney in the same over.
Durham’s opening pair appeared untroubled until Burnham slipped over, having advanced towards bowler Gurney, and was beaten by a direct hit from 15 yards by Wood at cover.
Stoneman pulled Wood for an impressive maximum and also hit six boundaries in his 50 before nicking Ball to Mullaney at second slip
In deteriorating light Borthwick reached his own 50 from 72 balls, 11 of which were hit for four. Durham, without a win in their last six matches, will begin the second day just 30 runs adrift.