The Spaniard, last year's championship runner-up, entered Losail on the back of an exceptional pre-season when he and Honda often appeared the class of the field.
While he could not match Lorenzo in qualifying - and only rescued a front row starting slot with a last-gasp flyer - Pedrosa said he had been confident of fighting for victory, only for Lorenzo to ease away into the distance.
Pedrosa was ultimately pushed back to fourth behind Valentino Rossi and Marc Marquez.
"Even though things went well in the pre-season the first race did not go as we expected," Pedrosa wrote in his Repsol blog.
"On Saturday, and in the warm-up as well on Sunday, it seemed that we had enough pace. Then, when the race started, Jorge was very fast from the beginning.
"Behind, me, Marc and Valentino were pushing hard also, but we did not quite get the set-up right and so we could not finish on the podium."
After his 2012 title bid was ultimately undone by his start to the season, Pedrosa acknowledged fourth was far from ideal but said he was not too disheartened given his specific set-up complaints.
"As you know, we did not get off to the start we would have liked," he admitted.
"The whole weekend and the level of grip was not so good. I tried to change my riding style to protect my position, but there was not enough grip in the rear end.
"The positive thing is that we have learnt a lot in this race and we are already thinking about the next GP in Austin in two weeks."