The 28-year-old former world champion will not win Commonwealth gold for a second successive Games as a string of injuries in recent months caught up with the Welshman.
Greene - who clinched the world title in Daegu three years ago - has struggled for fitness this year and it showed as he faded badly towards the end of his heat.
A time of 50.36 seconds could only secure him a fifth-place finish, with Greene bemoaning a lack of sharpness afterwards.
"I knew I was playing catch up from a few months ago, I didn't expect to be here but my mindset did shift a bit and I wanted to make the final but ran out of steam, sadly it wasn't to be," he told BBC Sport.
"I was provisionally selected for the European Championships but I don't think I'll make the squad now.
"I'm not fit enough really, it has been frustrating but I'm happy to have given it a shot."
In the pool, Meaghan Benfeito and Roseline Filion of Canada took gold in the synchronised 10m platform final courtesy of a score of 310.65 points as their experience paid dividends.
That tally was enough to edge English duo Sarah Barrow and Tonia Couch into second with Malaysian duo Pandelela Rinong Pamg and Nur Dhabitah Sabri taking bronze.
In the artistic gymnastics all-around final at the SSE Hydro, England's Max Whitlock clinched gold with a total score of 90.361.
Whitlock picked up two bronze medals at the London 2012 Olympic Games, and impressed on the floor and the pommel horse to see off Scotland's Daniel Keatings.
Keatings claimed silver while Whitlock's 18-year-old compatriot Nile Wilson completed the podium.
Having defended her singles title, squash gold medallist and world number one Nicol David saw her doubles hopes with Low Wee Wern dented by Indian pair Dipika Pallikal and Joshana Chinappa.
David and Wee Wern were beaten 11-8 11-5 but can still secure a last-eight spot with victory over Sri Lanka later on Wednesday.