The race, due to have begun on Sunday night, was re-scheduled for 9pm Monday local time (2am Tuesday Perth time) after it was cancelled when torrential rain fell just minutes before the start.
Stoner had dominated all practice and qualifying sessions on his Ducati and had been set to start the race from pole position.
But officials had no choice but to cancel the race, leading to an organisational headache and massive extra costs in a sport desperate to save money.
"It's just unlucky with the weather,'' said Stoner, the 2007 world champion, who was bidding for a third successive win in Qatar.
"It can be a good idea or it can be a bad idea to race on Monday. A lot of money has been spent on keeping people here at a time when we are trying to cut costs.
"It's disappointing it's happened like this.''
"We wait six months for the first race of the season. But when you decide to have a night race, it's risky. No-one expected these conditions in Qatar."
Circuit organisers were preparing to use three special machines to clear the track of excess water throughout the day.
