He will be joined by fellow Australian Cameron McEvoy who had the fourth fastest time.
They’ll be chasing down American Nathan Adrian who won the gold at the London Olympics and Canada’s Santo Condorelli in third position in tomorrow’s final.
Chalmers now has swimming’s biggest names in his sights after earlier upstaging Australian teammate McEvoy in the 100m freestyle heats overnight, Australian time.
The 18-year-old set a junior world record to top the 100m heats, with gold medal favourite McEvoy cruising to be fourth quickest.
Chalmers’ new personal best time of 47.90 seconds would have won silver at the 2015 world titles in Russia.
Remarkably he blew away defending Olympic champion Nathan Adrian of the United States in his heat, despite being last at the 50m turn.
Asked if he was concerned at the 50m mark, a relaxed Chalmers said: “No, not at all.”
“My back end is my strength… I purposely went easy on the way out, just cruised through and then tried to catch Adrian’s wave,” he said.
“It’s just a heat. It’s about progressing through the rounds.”
McEvoy warned that Olympic rookie Chalmers was only just getting warmed up.
“He just snuck under 48 seconds for the first time which is amazing (but) I definitely think he has more in the tank,” he said.
“He is handling (his first Games) so well… he has been so easy going.”
McEvoy arrived at Rio as the red hot favourite after clocking 47.04 at the April trials – the third fastest of all time and quickest outside a supersuit.
But the form guide was thrown out the window in the heats as American Adrian (48.58) scraped in to grab the 16th and final semi-final spot.
World champion Ning Zetao (48.57) of China also had some anxious moments, finishing joint 14th.
“It’s exciting to see the depth in the 100m freestyle,” McEvoy said.
“It was pretty cut throat there at the end from eighth to 25th – the semi-finals should be amazing.”
Meanwhile, Australian swimmer Emma McKeon won the bronze medal in the women’s 200m freestyle, adding to her gold medal as part of Australia’s victorious 4x100m relay team on the weekend.
The Olympic debutant produced a strong last lap in the 200m freestyle final, won by American Katie Ledecky with Swede Sarah Sjostrom taking silver.
“I think that is what I have proved to myself in the end that I can be tough in an Olympic final where there is a lot of pressure,” McKeon said.
Australian Bronte Barratt finished equal fifth.
McKeon led the field at the first turn, and held that spot at the 100m mark before being overtaken by Ledecky and Sjostrom.
The 22-year-old’s medals continue a rich family swimming history – her brother David is also competing at the Rio Games.
Her father Ron swam at the 1980 and 1984 Olympics and also won four Commonwealth Games gold medals, her mother Susie also is a Commonwealth Games swimmer and Susie’s brother, Rob Woodhouse, was a bronze medallist at the 1984 Los Angeles Games and also raced at the 1988 Seoul Olympics.
Meanwhile, Australia’s Daniel Smith, Mack Horton, Jacob Hansford and Thomas Fraser-Holmes (seven minutes, 07.98 seconds) were sixth fastest qualifiers for Tuesday night’s 4x200m freestyle final.
Australia’s Madeline Groves (fifth) and Brianna Throssell (10th) cruised into Tuesday night’s 200m butterfly semi-finals.
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