The 19-year-old Australian was some way off his world record of three minutes, 40.08 seconds, but still managed to out-perform his rivals.
Thorpe was feeling the effects of a busy summer which included the Commonwealth Games in Manchester, where he won six gold medals.
And he insisted afterwards that finishing one-two with Australian team-mate Grant Hackett had been more important than a world record.
"Grant and I just wanted to get Australia off to a good start. I didn't think it was in my best interests to try to do sub-3:40," he said.
Thorpe later anchored Australia to gold in the 4x100 metres freestyle relay.
And the triple Olympic champion stressed that he was putting the team before individual achievements.
He said: "I took a step back in the 400 metres because I wanted to swim a controlled race. My preparation tonight was more for the 4x100 metres."
Australia have now recorded four straight wins over the US in the 4x100 metres freestyle.
Thorpe believes the key to their success is teamwork.
He said: "We might not always be the strongest swimmers but we have this great pride that makes us a very successful team."
Dream finale
Hackett, who gave Thorpe a lead of 0.26 seconds going into the anchor leg of the relay, agreed.
"If you're going to think as an individual, you're going to compete as an individual. Our attitude is to work as a team and to try to gel together 100% of the time," he said.
And Australia's women emulated the men to also take gold in the 4x100 metres freestyle ahead of the US.
Jodie Henry, Alice Mills, Petria Thomas and Sarah Ryan erased the memory of a sixth-place finish in Fukuoka.
"It was so important not to be intimidated by the U.S. team as we have done in the past," said Ryan, who hinted she may retire from swimming after the championships.
"To win this tonight was so sweet, it could be the perfect way to go out."