The new ball proved more of a threat in the evening than the morning at Chester-le-Street as Division One leaders Middlesex replied to Durham's 259 by slipping to 11-2.
Corey Collymore had taken two wickets in two deliveries with the second new ball to finish with 4-61 as Durham's last four wickets went down for 29.
Then Graham Onions knocked back Sam Robson's off stump with the sixth ball of the reply and Chris Rogers was lbw to Callum Thorp in the next over.
With leading wicket-taker Tim Murtagh on Ireland one-day duty against Pakistan, Middlesex struggled in the morning to capitalise on winning the toss in conditions expected to favour the seamers.
Collymore had Mark Stoneman caught behind in the sixth over, but there was no further success before lunch.
They bowled with more purpose afterwards and reduced Durham from 108-1 to 149-5 before Phil Mustard made the top score of 62.
Durham failed to capitalise on three dropped catches, with skipper Paul Collingwood surviving an edge off the first ball he faced only to miscue the second to midwicket. Keaton Jennings and Ben Stokes survived straightforward slip chances with opener Jennings sticking around until early afternoon in sharing a second-wicket stand of 101 with Scott Borthwick.
Continuing in his new role at number three, Borthwick pulled Gareth Berg for his ninth four to reach an 86-ball half-century, only to drive at the next ball and edge to wicketkeeper John Simpson. Jennings was lbw to Collymore for 38 and Stokes inside edged a drive off James Harris to be well caught by Simpson, diving to his right.
Collingwood became Harris's second victim, attempting to pull, before Will Smith and Mustard put on 55, while Smith grafted for 107 balls to make 37 before both he and Gareth Breese were victims of edged catches when driving loosely.
Once the new ball was taken Thorp never looked surviving against Collymore and had his leg stump knocked back, then Wood was lbw. Mustard drove Harris back over his head for his sixth four to reach 50 off 97 balls then stepped back to loft a four over extra cover. But he gave Harris a third wicket when he drove to long-on, where Toby Roland-Jones held an excellent catch.