Graham Onions was the last man out to Sidebottom’s second ball, caught by Gale at mid off for 6, leaving Liam Plunkett unbeaten on 65 and Durham all out for 327.
Onions couldn’t really have asked for a better start to his return to the field– a wicket with his second deliver with Adam Lyth hitting ball directly to Ben Stokes at mid wicket with Yorkshire 0-1 after 1.2 overs.
Antony McGrath added 15 before he was trapped lbw off Callum Thorp in the tenth over with Yorkshire 43-2.
A flurry of extras added to the Yorkshire total but the attack re-adjusted, with a bit of spin and a few overs from Benkenstein before lunch Durham tried to restrict the run rate. At the break Yorkshire were 93-2.
Last ball of the third over after the interval, Gale spoons it up to Ian Blackwell at mid on off Onions and is dismissed on 16 leaving Yorkshire 100-3.
Onions picked up a third wicket when Bairstow was given out lbw without scoring and then went to pick up a fourth when Joe Root was caught behind five short of his maiden Championship fifty, leaving Yorkshire in a little bit of trouble at 113-5, with Brophy and Rashid in the middle.
The visitors stalled a little with Blackwell keeping them tied down at the Football Stand End and he eventually picked up a wicket when Rashid (7) edged the ball to Di Venuto in the slips. His replacement, Richard Pyrah was dismissed the following over, out lbw from a delivery that kept low from Thorp and Yorkshire then reduced to 125-7.
The hosts lost their sixth wicket in just 27 runs when Sidebottom was out lbw off Thorp for only 2.
Onions claimed his fifth wicket of the innings, his first since June 2009 and his fourth against Yorkshire in Championship cricket, when Patterson was caught behind for just one leaving Yorkshire 131-9.
A bowling change brought Scott Borthwick on for the 59th over and he picked up the final scalp of the day with the first delivery of his second over when Moin Ashraf was caught by Stokes for 5.
Durham decided to extend their lead of 180 and therefore not enforce the follow on.
Di Venuto and Smith opened but it was the former that was out first, caught by Pyrah at first slip off Sidebottom for 12 in the ninth over.
Another quick wicket fell when Smith was given out lbw to Ashraf for 8 reducing Durham to 25-2.
There was a bit of a scare in the 16th over with a run out attempt against Stokes by Rashid but the umpire was well placed enough to dismiss the appeal, next ball Stokes smashed a boundary past a fielder in the deep to see Durham past the fifty mark.
Stokes (28) was bowled the next over by Patterson bringing stand in skipper Dale Benkenstein to the middle to join Muchall (4*).
Bad light brought play to a halt at 5.50pm, losing a potential 10.1 overs, with Durham leading by 243 on 64-3, Muchall 6* and Benkenstein 9*.
Check out the action as it happened via our Live Match Chat page (www.durhamccc.co.uk/live-match-chat) or wait until tomorrow when you can take a look at the day two highlights which will be posted at www.durhamccc.co.uk/durhamtv/highlights