The 29-year-old, who quit the sport five years ago, clocked a time of 56.33 seconds at the World Cup meeting.
Thorpe, who is bidding to swim at the 2012 Olympic Games in London, had earlier qualified sixth fastest.
He will race in the 100m butterfly on Saturday, before heading to the World Cup meets in Beijing and Tokyo.Continue reading the main story
Gold 200m freestyle, 2004
Gold 400m freestyle, 2004
Gold 400m freestyle, 2000
Gold 4x100m freestyle, 2000
Gold 4x200m freestyle, 2000
Silver 4x200m freestyle, 2004
Silver 200m freestyle, 2000
Silver 4x200m freestyle, 2000
Bronze 100m freestyle, 2004
Thorpe bettered his qualifying time of 56.74 in Friday's individual medley final but was well off the pace set by South African Chad Le Clos, who won in 53.06.
After a strong start on the butterfly leg, Thorpe lost ground on the backstroke in the second leg and never challenged in an event he rarely competed in prior to retirement.
The Australian has been preparing for his comeback under the guidance of Russian coach Gennadi Touretski in Lugano, Switzerland.
Thorpe has publicly played down any hopes of returning to the dominant position he once held, with his focus on qualifying for a strong Australian Olympic squad next year.