She finished four seconds behind Tamara Gomez Garrido of Spain, who took gold in one hour one minute 42 seconds.
Kretz, a 21-year-old from Blainville, Que., was sidelined for most of last season due to injuries. She was coming off a Continental Cup race victory a week ago.
"I was feeling strong and confident. My training has been going very well here in Australia." said Kretz. "Winning last week just confirmed my fitness was coming around. I was confident that I could execute a good race. It feels great to get a medal on a classic World Cup course here in Mooloolaba.
"The race is always hard here and the field always strong. It's a big World Cup so it feels good to finish with a medal."
Australia's Ashleigh Gentle was third in 1:02.01. The race was over the non-Olympic distance of a 750-metre swim, 20-kilometre cycle and five-kilometre run.
"The swim conditions were pretty rough, but I've been training in worse conditions in Wollongong so I wasn't too worried," she said. "When the pack caught us, I just focused the rest of the bike on positioning myself well in the technical sections and keep the pace nice and high."
Kretz's only other World Cup podium appearance came nearly two years ago when she took gold in Edmonton.
Edmonton's Paula Findlay was 11th and Sarah-Anne Brault of Quebec City was 13th.
David Hauss of France won the men's race in 55:22. He finished two seconds ahead of Jacob Birtwhistle of Australia.
Vicente Hernandez of Spain was nine seconds off the lead in third place.
Michael Lori of Tecumseh, Ont., was the top Canadian in 17th.
With files from The Associated Press.