The five-times Olympic champion's exit, which followed his failure in the 200 freestyle earlier in the trials, robbed the meeting of its headline act, but Stephanie Rice went some way to easing the crowd's disappointment by clinching the 200 individual medley title in the evening session.
The triple Olympic champion eased her way into the race and reeled in world silver medallist Alicia Coutts in the final lap to secure her second title of the meeting despite swimming through the pain of an injured shoulder.
Rice, who captured the 400IM title on the opening day, posted a time of two minutes, 9.38 seconds and ensured she will defend both her Olympic medley titles at London.
"I was confident standing behind the blocks before this race," Rice told reporters at the South Australia Aquatic and Leisure Centre.
"I felt like I wasn't moving in the last 25 (metres), but obviously I was ... I'm really happy to come away with a PB (personal best) in these suits, (and) more than anything, just to execute the race I wanted to execute."
The 23-year-old's personal best of 2.07.03 was set in a now-banned suit at the 2009 world championships in Rome.
Thorpe earlier won his heat in the morning session but finished 21st in the timings behind pace-setter James Magnussen in his last-chance saloon for London.
His time of 50.35 seconds was his best since returning to competition in November but more than two seconds shy of the world champion's.
"This is... it's tough. It's hard coming to this competition and really, you know, failing in what I set out to do," Thorpe said.
"I'm disappointed that I really haven't been able to race in a way that's reflective of the work that I've done and how I've trained.
"But I don't regret giving this a go. Compared to how I've raced before, how I've competed and the success that I've had, this does look like doom."
In Thorpe's absence, the spotlight rightly shifted back to Magnussen in the 100 freestyle, as Australia's first world champion in the blue riband sprint charged into the final with a time of 47.93 seconds.
The confident 20-year-old eased up in the last 25 metres to be marginally slower than his 47.63 that won him the gold at Shanghai, but set his sights on bettering Brazilian Cesar Cielo's world record in Monday's final.
"I'll certainly be going for it, but you just don't know until the day, it's got to be one of those swims that feel like you're floating, I guess," the swimmer nicknamed "the Missile" said.
"The earlier I can put a good time on the board before the Olympics the more the rest of the world will sit up and take notice."
The former bad boy of Australian swimming, Nick D'Arcy won the 200 butterfly title just outside his Australian record to book his London ticket, four years after being kicked off the Beijing-bound team for punching fellow swimmer Simon Cowley at a Sydney night club.
"It's been a pretty rough ride at times but I think I've come out the other side of adversity ... and put myself in a good position to be at the Games," he said, before focusing on a potential showdown with American great Michael Phelps at London.
"For me it would be a fantastic way to probably end my career (racing Phelps) because it's such a good rivalry that I get from him and he's such a fantastic athlete."
World silver medallist Kylie Palmer qualified for the Olympic 200 freestyle with a runner-up finish in the final behind Bronte Barratt, her team mate in the gold medal winning 4x200 freestyle relay at Beijing.
Two-time Olympic 100 medley relay champion Jessicah Schipper qualified fastest into the 200 butterfly final, while Beijing silver medallist Brenton Rickard topped the timesheets in the 200 breaststroke semi-finals.
Magnussen's bid to break Cielo's record in the 100 freestyle final highlights day five on Monday, with triple Olympic champion and comeback kid Libby Trickett making a last-ditch attempt to qualify for London in the 100 freestyle.