Mr Joyce applauded the Fair Work Australia decision, saying it brought "certainty'' back to the business after the bitter labour dispute.
"Now we can get on with having a sensible negotiation, both parties are incentivised to negotiate before binding arbitration, but we know with certainty our customers are not going to have the disruption that they've seen over the last few months. Our employees are going to have certainty that this will end, either way, in the next 21 days.''
Mr Joyce said he had no alternative but to ground the company's entire fleet, but was adamant no decision had been made to do so at the company's AGM on Friday.
"That was the only way we could bring this to a head. It has brought it to a head, it has resulted in us now sitting down and having an ability to negotiate a sensible settlement for all parties.
"I'm disappointed and I apologise to our customers that we had to get to this stage but we're disrupting a lot less customers by doing it this way than this dispute lasting for another year and tens of thousands of customers every week getting impacted.''
He was confident the Qantas brand would bounce back after the dispute, which led to the cancellation of 447 flights and cost about $A20 million ($NZ26m) a day while planes were grounded.
"I think the Qantas brand is an amazingly resilient brand and we've gone through very significant industrial disputes before.
"I think we will rebound, we're going to plan together to recover and focus in on ... the customers over the last few months who have been disrupted by union activity _ get their loyalty back.
"Now we can move on with certainty, we can focus on serving our customers, we can focus on building a stronger Qantas for our shareholders, we can focus on building a Qantas that is strong and stable and a success story for Australia and around the World.
Trans-Tasman flights were yesterday running as usual, as an Auckland-based subsidiary Jetconnect runs flights under the Qantas banner.
Air New Zealand has been working with alliance partner Virgin to allow the Australian company to help some stranded passengers.
Australasia general manager Bruce Parton said Air New Zealand was working to free up six to eight aircraft and was organising cover for baggage-handling duties, which are covered by Qantas.
Mr Parton said putting on extra Air New Zealand planes would allow its partner Virgin to divert aircraft to Australian domestic routes in a bid to limit disruption ahead of Tuesday's Melbourne Cup.
Mr Parton flew to Sydney yesterday afternoon to work on contingency plans. He said the airport's Qantas check-in area was "utter chaos''.
"It's 20 feet deep with people screaming and yelling. There's a lot of anger and angst, the customers are pretty unhappy with how they've been treated.
"When I'm talking to the Qantas customers, what they're staggered with is the speed at which this was bought in. No one got any warning. They just feel like they've been treated with disdain.''
He said people he'd talked to would remember the incident, and there would be long-term damage to the Qantas brand.
