The Yamaha rider moved methodically to the front after starting fourth on the grid, only suffering one late wobble while clear at the front.
It was the Spaniard's fourth win in six races this season, and he has not finished outside the top two yet.
"I was fifth or sixth (after the start) and I didn't want to make mistakes so I had to wait a little bit," Lorenzo said afterwards. "This victory is fantastic, the season we are doing is just perfect, we can't ask for more."
Stoner said he had realised he could not win from lap one when he saw how much more grip Ben Spies had on the Yamaha.
"Even when I went around to the grid the bike didn't feel right so we made another change before the race and it was just horrible. We just struggled the whole race," he added.
"I knew if they got past it was going to be one hell of a try to keep up and we just couldn't."
But the home crowd's real hero was Cal Crutchlow, who finished a brilliant sixth after starting from the back of the grid.
Crutchlow broke his left ankle crashing in practice and took no part in qualifying, but defied the pain with a magnificent performance.
"It's been a tough weekend. Missing two hours of track time to these guys is a disaster so I'm pleased. I'm just emotionally drained," he said, adding he would have finished on the podium had he not started from the back.
"They told me I wasn't allowed to ride, at the hospital. So I left the hospital, lied a little bit when we got to the circuit and the medical staff did great here."
Pole-sitter Alvaro Bautista had to settle for fourth, while Lorenzo's Yamaha team-mate Spies was fifth.
James Ellison claimed a creditable points finish on the Paul Bird Motosport CRT machine.