The Aussie four of William Lockwood, James Chapman, Drew Ginn and Joshua Dunkley-Smith headed into the final having already handed Triggs Hodge and co a defeat in the semi-final.
And, while it was a far closer race second time around, Australia repeated the trick on the closing day in Germany to record a winning time of 6:10.28minutes.
Britain, who had won gold at the last two World Cup regattas in Lucerne and Belgrade, were nearly a second behind in 6:11.15 with Belarus taking bronze.
But Triggs Hodge - joined by Tom James, Alex Gregory and Pete Reed in the four - insists the sole thing they will be doing from the defeat is learning from it.
"We are still part of an incredibly successful GB squad now it's the same as always. We go away to training camp and will put in the hard work and attention to detail in the six weeks before the Games begin", said Triggs Hodge.
"We found a different rhythm and that was a lot better. I think we have learnt a lot here and we can take that away to training camp in the next six weeks."
Britain won eight medals on the final day in Munich, adding to the three on Saturday from the Paralympic and non-Olympic classes, with the men's four the only crew to take silver.
The women's pair of Helen Glover and Heather Stanning and the women's double scull of Katherine Grainger and Anna Watkins contributed two of the golds.
And, while the men's four couldn't complete a clean sweep of World Cup gold medals this year, Glover and Stanning and Grainger and Watkins' wins did exactly that.
The British lightweight men's four of Richard Chambers, Peter Chambers, Chris Bartley and Rob Williams claimed the third gold after an eye-catching performance in Germany.
And Britain's medal haul was completed by the women's quadruple scull and the men's and women's eights, who all took bronze, while Alan Campbell followed suit in the men's single scull.
However there was disappointment for the reigning Olympic lightweight men's double scull champions Mark Hunter and Zac Purchase as they finished well outside the medals in sixth.
There was similar heartache for four other British boats with Graeme Thomas having to settle for fourth nearly six seconds behind Campbell in the single scull.
Bill Lucas and Sam Townsend in the men's double scull also finished fourth as did Stephen Rowbotham, Tom Solesbury, Charles Cousins and Matthew Wells in the quadruple scull.
Sophie Hosking and Katherine Copeland completed the British fourth-place finishes in the women's lightweight double scull with Imogen Walsh and Andrea Dennis sixth.
Britain did win the overall World Cup title though and British performance director David Tanner was satisfied with what he saw - particularly from the women.
"We've actually had a good day with some excellent results. Many crews have stepped on from the last World Cup. We've also had some disappointments," said Tanner.
"I'd like to say a big congratulations to the women's squad on their medals. There were outstanding performances in the women's double and pair and also from the lightweight men's four."
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