The 24-year-old completed the 1.5km swim, 40km bike and 10km run in 2:03.53hours to finish as the runner-up 22 seconds behind German training partner Anne Haug in Mooloolaba.
Stimpson was part of a small group that stayed together on the bike after Olympic bronze medallist from Beijing 2008 and home hope Emma Moffatt led out the swim.
They had established a lead of over three minutes by the start of the run with Haug, Stimpson, Moffatt and New Zealand's Andrea Hewitt soon breaking away.
Hewitt dropped with 5km to go with Haug kicking clear of Stimpson with a kilometre remaining to win her first World Cup race while Moffatt was third 31 second adrift.
Stimpson will now turn her attentions onto the opening two rounds of the World Series, the first in Auckland next month and then second in San Diego less than two weeks later.
And, after following up her win at the Devonport OTU Sprint Championships last month with second at the World Cup opener, Stimpson is desperate to transfer her form onto the World Series.
"To be second and on the podium on one of the hardest courses of the year is great. I have like a second family out here so it is awesome to race well in front of them," said Stimpson.
"I train with Anne day in day out and I know how strong she is, if I am running with her I know I am running well. She just had me at the end, I am working on that it is a work in progress.
"I am now off to New Zealand and then San Diego, I really want a strong finish in the World Triathlon Series this year. That is the big goal."
Stimpson was joined in Mooloolaba by fellow Brit Hayes, who finished 37th in the London 2012 Olympic triathlon as Alistair and Jonathan Brownlee won gold and bronze respectively.
He placed eighth in his first major race of the season in Queensland after clocking a time of 1:56:19 as Olympic silver medallist from London 2012 Javier Gomez took victory in 1:54:32.