The race was a rather one-sided affair with the Australian finishing well clear of the field, with Lorenzo coming in second and Ben Spies completing the podium.
23-year-old Italian Marcon Simoncelli started the day on pole but had a disappointing race and eventually finished sixth after an uncharacteristically slow start.
The overcast condiditons in Barcelona made the right tyre choice essential on an increasingly slick track and Stoner appeared to have chosen correctly as he soloed to victory.
Stoner is now only seven points behind Lorenzo in the standings and the 2007 World Champion was understandibly delighted with the victory and said his race went exactly to plan.
"Jorge got off to a good start and I had to wait until the end of the first lap to overtake him and then he couldn't stay with me, fortunately" Stoner told reporters.