Attempting to bat out the entirety of a 98-over day from a starting point of 18 for two, Roy was clean-bowled for a battling 31 before England's hero at Headingley, Stokes, fell for just one to a thin edge.
Cummins has now taken all the wickets in England's 87 for four, leaving Joe Denly, who gritted his way through the morning session for an unbeaten 48, to lead the resistance alongside Jonny Bairstow.
In their stead it fell to two men with considerable points to prove, and who had swapped positions for this match to try and recapture their best form.
There were a couple of lbw shouts against Denly in the opening overs, both sliding down leg side and neither tempting Tim Paine into wasting a review, while Roy was able to coax the first big roar from the 22,000-strong crowd when he tucked the ball through mid-wicket for four.
Both men were playing cautiously until Denly's patience wavered, chasing a wide one from Mitchell Starc and seeing a wild outside edge sail over the cordon. To even consider playing at such a ball was an error, but he survived with nothing worse than a lesson learned and four runs to his name.
It took Paine just eight overs to send for Nathan Lyon's spin and Denly greeted him by sweeping hard to the boundary. There were a couple of nervy moments, Roy almost offering a bat-pad chance and Denly's slog-sweep landing just in front of the fielder, but otherwise all was well.
By the time Roy leant on a nicely-timed cover drive off Starc an hour had passed and England had moved along to 56.
Australia were searching for a breakthrough and, after 18 overs and 80 minutes, Cummins provided it. It was another fine delivery from the world number one, seaming in between Roy's bat and pad and hitting off stump.
Roy's work was done and his departure brought Stokes to the crease, to the expected deafening welcome. He lasted just 17 deliveries, though, caught in two minds by one that moved back in and flicked the inside edge of an attempted leave.
Umpire Marais Erasmus was not sure, but Australia knew they had their man and Stokes opted to walk before DRS was required.