Pedrosa had qualified his Honda on pole with a record-setting pace on Saturday, but he was beaten by Lorenzo at the start and sat behind the Yamaha rider for the duration of the grand prix.
He shadowed his fellow Spaniard throughout - much like in the last race at Mugello - but dropped back in the closing stages and fell under attack from his team-mate Marc Marquez.
"It was not like yesterday," said Pedrosa after the race.
"I was riding smooth but when I tried to push a little and step up the rhythm I started to feel like the front tyre was giving up almost every corner.
"I waited a little more, but so many laps after it was the same thing and I was struggling a lot in the corners."
Pedrosa maintained losing out at the start was not crucial, claiming it was more his lack of performance that made the difference in the battle at the front.
"The start was not bad, it was good enough," he added. "I was quite OK and just trying to let the laps come down.
"[But] I could not go very fast in the last two corners, so into the straight Jorge had a little gap on me and it was hard to make a move on him.
"Second is good for the championship, but I think today we could have done a little better."