Cavendish suffered cuts and abrasions to his face and body in a crash during Wednesday's second stage, and was left trailing late in Thursday's finale as the peloton tackled a hilly 21 kilometre (13 mile) circuit three times.
Riding in near 40-degree Celsius (101 Fahrenheit) temperatures, Cavendish's task to finish before the cut-off time was made harder after police reopened the road to public use once the main peloton had passed.
A 15-time stage winner in the Tour de France and one of the biggest names in the sport, the Isle of Man rider erupted after trailing home 12 minutes behind Australian stage winner Michael Matthews of Rabobank.
"I did the whole last lap on open road, you had to stand on all sides of the thing and stop for traffic," blasted Cavendish.
Asked if he had to negotiate much traffic, Cavendish replied.
"Quite a bit yeah, you know, more than you want in a professional race I think."
Race director Mike Turtur had already been forced on the defensive Wednesday after gravel patches were blamed for several of the crashes that marred the closing kilometres of stage two.
Turtur said an emergency meeting would be called to find out why the "green light vehicle", which normally sits behind the last rider at the back of the race convoy, had moved ahead of Cavendish.
"We've had a policy in place whereby the green light vehicle is the last vehicle on the road behind the last rider, for 13 years," said Turtur.
"For whatever reason, our understanding is that green light vehicle was called forward of the Cavendish group with about 10 kilometres to go and we don't know the reason why.
"Until we know how and why, I can't make any further comment -- but it's not the policy we've had in place for 13 years, it's never happened before.
"It's not good, but sometimes these things happen....
After a meeting with police, Hitaf Rasheed, the general manager of organiser, Events South Australia, said: "We have met with SAPOL (South Australian Police). We've been advised that a decision was made regarding the green light vehicle in the interest of safety.
"The green light vehicle will continue to signal the end of the race and follow the last rider across the finish line."
Cavendish said he felt sore and lethargic due to a combination of fatigue and having to take painkillers to numb the pain of Wednesday's crash, which left him with a gash above his left eye.
"I can't complain really, it's just bike racing. You have good days and bad days," he said.
Painkillers "make you a bit lethargic and mess with your guts a bit, but it's the same for everybody. I'm just tired, a bit sore."
"Sometimes you come off OK, other times you come off pretty bad. I came off pretty bad, but in the grand scheme of things I reckon I've been pretty lucky."