Britain's Alistair and Jonathan Brownlee finished fourth and fifth respectively as Javier Gomez claimed a third successive World Series win of the season in Yokohama, Japan.
Defending champion Gomez beat fellow Spaniard Mario Mola in a thrilling sprint finish, with South African Richard Murray third.
In the women's race, Briton Jodie Stimpson - winner of the first two World Series events - finished ninth after a fall as American Gwen Jorgensen took victory.
Stimpson, 25, finished the race despite suffering a cut foot in her fall that required five stitches, but she maintained her lead in the overall standings.
Aaron Harris's sixth-place finish secured his place in England's Commonwealth Games team alongside the Brownlee brothers.
The race was part of Alistair's build-up to Glasgow 2014, which he will prioritise ahead of trying to regain the World Series title he won in 2009 and 2011.
He and Jonathan, 24, were among the leading group after the 1.5km swim and 40km cycle.
But Jonathan, Olympic bronze medallist at London 2012, fell back early in the 10km run, and 26-year-old Alistair faded on his return from the Achilles and calf injuries that kept him out of the first two races.
The Spaniards broke clear of Murray late on, before Gomez outsprinted Mola to win by one tenth of a second in one hour, 45 minutes and 31 seconds.
"It was the toughest race in a long time; I gave everything," said 31-year-old Gomez.
Alistair, the Olympic champion, said: "I've done a lot of training and didn't feel like I had my race legs on. The harder I worked the worse it got."
Jonathan failed to make the podium in the World Series for the first time in almost four years, while compatriots Adam Bowden and Grant Sheldon finished ninth and 13th respectively.
Like the Brownlees, Stimpson also well placed before the run, but tripped on a pedal as she ran out of transition with her bike.
Jorgensen dominated on the run to take victory in 1:58.38, with Japan's Ai Ueda second and Poland's Agnieszka Jerzyk third.
After Stimpson, Lucy Hall was the next highest Briton in 32nd place.
Meanwhile, British Para-triathletes won four golds across their events in Japan.
Four-time world champion, Faye McClelland had one of the toughest races of her career to overhaul team-mate Lauren Steadman in the final kilometre of the PT5 class with fellow Briton Clare Cunningham in third.
Phil Hogg and Jane Egan won golds in the PT1 class for wheelchair athletes while Dave Ellis was victorious in the visually impaired class.