Tomljanovic won the initial two games of the all-Australian second-round match on centre court on Wednesday night before succumbing to a right shoulder injury.
Leading 2-0 and with scores at deuce in the third game, the 32-year-old Tomljanovic called a medical time-out.
The world No.76, given a wildcard into the Adelaide WTA 500 tournament, was unable to continue and is now doubtful for the Open starting Sunday in Melbourne.
World No. 32 Joint, the nation's top-ranked female, advances to a quarter-final against Russian-born world No.8 Mirra Andreeva.
"I hope Ajla can get better really soon ... she seemed pretty bummed out that she couldn't play," Joint said.
"The AO's next week, so I'm sure that she wanted a couple more matches here."
Earlier Wednesday, Daria Kasatkina's hopes of a first title since her switch to Australian nationality were dashed with a second-round exit.
But Australian Open champion Madison Keys, also defending her crown in Adelaide, progressed to the quarter-finals.
Russian-born Kasatkina fell to world No.35 Jaqueline Cristian 6-4 6-0.
Eight double faults meant the newly minted Australian struggled to build her rhythm on centre court, with the match wrapped up in 91 minutes.
Former world No.8 Kasatkina, now ranked No.48, is on the comeback trail after ending her 2025 season in October to take a mental-health break.
She switched allegiances in March last year because of discrimination against the LGBTQI community in her native country.
Keys also had early serve troubles, and was forced to overcome seven double faults in the first set to secure a 6-4 6-1 win over Czech teenager Tereza Valentova.
"It was definitely frustrating," Keys said of her early service issues.
"I was able to figure that out and reel that back in the second set."
Also Wednesday, sixth-seeded American Emma Navarro breezed past Kazak qualifier Yulia Putintseva 6-1 6-4.
And Russian-born Diana Shnaider advanced with a 6-1 2-6 7-5 triumph against Czech Katerina Siniakova.
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