The Fair Work Australia tribunal, which delivered its ruling in the small hours of yesterday, ordered the unions to halt their industrial action and the airline to resume flying. The two sides have 21 days to reach agreement or face binding arbitration.
The dispute is about pay, conditions including job security, and Qantas' restructuring plans, which will cost 1000 jobs and see a new airline created in a cheaper Asian hub.
Joyce played down any longterm damage to the "Flying Kangaroo" brand. He said: "We will be doing all that we can to put things right."
Experts were divided over what impact it would have.
"It was a very shrewd move by their CEO to force the issue and stop the potential deterioration of the brand," said Mo Garfinkle, an airline consultant. "In the end, it will benefit Qantas financially."
But Henry Harteveldt, an industry analyst in San Francisco, predicts the shutdown will damage the Qantas name by hurting its reputation for reliability.
"A lot of travellers ... will book away to Virgin Australia, Air New Zealand and other airlines," Harteveldt said.
The resumption of flights was a relief to thousands of passengers, including John Madderon, who was stranded in LA on Saturday with his wife, Kathryn, and their three young daughters. Madderon is best man at his brother's wedding in Brisbane next weekend.
Qantas is still calculating the size of the domestic backlog, but its main rival, Virgin Australia, has been putting on thousands of extra seats.