The Mission, B.C., native finished fourth in his semifinal heat on Tuesday with a time of 48.21 seconds to advance to Wednesday's final.
"That hurt a lot," said Hayden, the 2007 world champion, competing at his third Olympic Games. "I know technically where I have room for improvement. I was a little too shallow coming off the wall so I had to nail that incoming wave and build up my speed a little bit more than I wanted to."
James Magnussen of Australia was the fastest qualifier in 47.63, Nathan Adrian of the U.S., second in 47.97 and Hanser Garcia of Cuba third in 48.04.
Earlier in the day, the three-time Olympian posted the fifth-fastest time in qualifying at 48.52 seconds.
Hayden went into the 2008 Summer Games as the reigning world champion in the distance but didn't qualify for the final and finished a disappointing 11th.
Meanwhile, Scott Dickens of Burlington, Ont., made it into Wednesday's semis of the 200-metre breastroke but didn't advance to the final. Audrey Lacroix of Pont-Rouge, Que., was 15th in the women's 200-metre butterfly heats but failed to advance out of the semifinals.
"I raced well and I fought hard," said Lacroix. "I feel I had the potential to make the final tonight but unfortunately the time wasn’t there. Racing in lane eight was good for me because it allowed me to stay focused on my race."
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