Cook qualified for the final with the fifth fastest time but could finish only sixth in 1min 0.99sec. The world record holder Brendan Hansen held off Japan's Kosuke Kitajima to take gold in a new championship record time of 59.37sec.
But Cook will waste little time dwelling on his performance in Montreal, with next month's Commonwealth Games trials in Sheffield already in his sights. Should he qualify, he will head to Melbourne as the No 1 ranked 100m breaststroker in the Commonwealth.
Kitajima, the 2003 world champion and 2004 Olympic gold medallist, finished second in 59.53sec while Hugues Duboscq of France was third in 1min 00.2sec.
Loughborough-based teenager Kate Haywood failed to make the women's 100m breaststroke final, missing out on qualification by a tenth of a second. Haywood finished fifth in her semi-final in 1:08.65 - nearly half a second slower than the British record she set early this year.
Jessica Hardy, of the United States, set a world record of 1min 06.2sec in her semi-final, clipping 0.17sec off the previous mark of 1:06.37 set by Australia's Leisel Jones at the 2003 world championships in Barcelona.
Michael Phelps bounced back from his surprise failure to make the 400m freestyle final to qualify for the 200m final in the fastest time of 1:46.33. Australian rival Grant Hackett was nearly one second slower, qualifying in the fourth fastest time.
Exeter's Liam Tancock, 20, underlined his potential with an impressive swim in the men's 100m butterfly semi-finals, but his time of 55.07sec was not good enough to qualify.
Elsewhere, South African Roland Schoeman smashed the world 50m butterfly record for the second time in two days, winning in 22.96sec.
Earlier, the Glasgow-based student Rebecca Cooke underlined her gold medal claims with an impressive show in the women's 1500m freestyle heats. Cooke, a World Championship bronze medallist in the 800m freestyle two years ago, qualified for the final in the fastest time.
Katie Hoff of the United States won the women's 200m individual medley final with the second fastest time in history, 2:10.41, just 0.69sec outside Wu Yanyan's 1997 world record.Reuse content