Cameron Prosser was second fastest with 49.87, while Tom D'Orsogna matched Roberts with 50.06.
A sluggish Thorpe turned last at the 50m and could only make up one place on the way home, recording a slower time than the 50.84 he swam in Italy last month and a lifetime away from his best of 48.56 he swam in 2004.
Thorpe's comeback in his bid to swim at the London Olympics continues on Saturday when he swims the 200m freestyle, which is considered his best chance of getting to the Games.
The 29-year-old has recorded modest results since returning to competition late last year and is racing against time to be competitive at the Olympic selection trials in March.
Also making a comeback, triple Olympic champion Libby Trickett qualified third fastest for the women's 100m freestyle final behind Melanie Schlanger who clocked 55.09.
Thorpe was still upbeat after the heat, saying he's still in heavy training although he admitted he has a lot of ground to make up.
"It's too slow for where I need to be in a couple of months' time,'' he said.
"It's not a setback ... I think nothing of this.
"I'm happy with where I'm at in training. That hasn't translated into anything in competition yet, but a lot of people are reassuring me it will.
"I really wanted two swims today ... I'll have another swim tomorrow and hopefully I'll swim better in that.''
- AAP