Parchment, who has run the world's leading time this year of 13.05 seconds, trod on a hurdle in the warm-up area shortly before the final, which was won by Andrew Riley.
"He was warming up and twisted his left ankle on one hurdle, which was lying around," Parchment's coach Fitz Coleman told Reuters. "The lighting could have been better at the warm-up track."
The Jamaican championships are doubling as selection trials for the Caribbean country's squad for the world championships in Moscow from Aug 10-18.
The 23-year-old Parchment could still be included for Moscow as the Jamaican athletics' federation rules allow him a wild card selection if he remains in the top three in the world.
"I'm happy to win, but it was really disappointing not to have someone as fast as Parchment in the race because he hurt his ankle during warm-up," Riley said after he clocked 13.33 to win the title ahead of Dwight Thomas (13.45).
"Having limited lights before a big hurdles final in the warm-up area was really not good."
Double Olympic 100 metres champion Shelly-Ann Fraser-Pryce made easy progress to Sunday's final of the women's 200 metres with the fastest time in all three semi-finals.
Fraser-Pryce, who holds a wild card entry to the 100 in Russia, cruised to 22.64 seconds in the first semi-final, while Beijing Olympics 100 silver medallist Sherone Simpson won the second in 22.85. Anniesha McLaughlin won the third in 22.88.
In the men's' 200, 2011 world championships finalist Nickel Ashmeade clocked a brisk 20.07 seconds to lead Olympic bronze medallist Warren Weir 20.27 into Sunday's final.
World and Olympic champion Usain Bolt has a wild card entry into the event in Russia.
American collegiate (NCAA) 800 metres champion Natoya Goule became just the second Jamaican female to qualify for the world championships in the event.
Goule lead from start to finish to clock a career best one minute, 59.93 seconds to win the event in the absence of national record holder Kenia Sinclair.
"I was concentrating on making the "A" qualifying standard, so when I came through the first lap in 58.1 seconds I knew I was on target to dip below two minutes for the first time," Goule said.
"That was the pre-race strategy given to me by my coach and it worked."
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