Championship leader Lorenzo led the first 21 laps of the race under increasingly heavy pressure from Stoner before the Honda got past.
"I knew Casey was strong and was becoming stronger and stronger every lap," Lorenzo admitted.
The Spaniard reckoned his tyre choice played a part, as he joined most of the frontrunners in using a hard rear Bridgestone while Stoner ran the soft version.
"Normally it's the hard tyre that is coming better in the middle of the race, but this time it was the opposite," said Lorenzo. "It seems that the soft one was becoming better and more consistent."
But Lorenz conceded that the main factor in the result was that Stoner's riding had been impeccable.
"Anyway today, Casey was the best," said Lorenzo. "He was the fastest one, the most consistent one. It was not my day, it was the day of Casey."
Stoner said the fact that he took a different tyre strategy to his main rivals made his victory in the Laguna Seca MotoGP race particularly satisfying.
The Honda rider has struggled with Bridgestone's revised hard tyre and chose to use a soft rear for the United States Grand Prix, in contrast to all the other frontrunners.
But Stoner was able to overtake team-mate Dani Pedrosa and Yamaha's Jorge Lorenzo and score his fourth win of the 2012 season.
"We knew that we were struggling with the hard tyre a little bit, but we have been over the past races," said Stoner. "I just can't get it working so well and can't get it up to temperature.
"At the same time, with the soft tyre we knew we had to be a little bit gentle. If I was pushing on it really hard and spinning it the whole race, it wouldn't have lasted."
Stoner admitted that his ideal tactic had been to make an early break and use his additional grip before later defending a lead, rather than having to come from behind.
"I tried to get to the front as soon as possible. Unfortunately Dani and Jorge got past me at the beginning," he said.
"My plan was to get a good start and see if we could get a small gap with the extra grip. But Jorge was riding some good fast lines and it was a little tricky to go off-line and overtake.
"So I sat back, tried to cool the tyres a little bit, tried to give it a bit of time and give them a break, and slowly pick up the pace again rather than cooking them. We got a little bit more grip out of them and kept it through to the end, made some nice moves during the race.
"I'm very, very happy with the way it all turned out for us and it was nice to do something different to everybody else."
The result keeps Stoner third in the championship, but he has reduced his deficit to Lorenzo to 32 points.