The Boeing 777 flying from Vancouver to Sydney joined an Air New Zealand Airbus A320 in the initial search for the damaged boat.
Captain Andrew Robertson said the airline was approaching top of descent and talking to air traffic control in Brisbane at 8.18am when it was asked to assist in the search.
The flight crew programmed the coordinates of the stricken yacht into the aircraft's flight computer and determined it was about 160 nautical miles (296km) further out from the coast than the 777 but that the aircraft was enough fuel to reach the location..
"We were at 38,000ft and we just kept going down," said Captain Andrew Robertson. "I knew we would have to get really low and we got down to 5000ft above the water as we approached the area.
"I had already made a PA announcement telling passengers what we were doing and as we got into the area, I said: "We're coming into the search area, please everybody look out to the window and if you seen anything let us know.
As the aircraft executed a right turn back towards to Sydney, the first officer spotted the boat but was unable to see anybody on the deck.
The aircraft had arrived about 20 minutes after the emergency beacon was activated but did not pick up a signal until it was a mile from the boat and then heard only sporadically.
"It was a very weak signal and he was very lucky to be located," said Capt Robertson, said.
The crew decided on another, lower pass at 3700ft and spotted what was initially identified three people, although two of them turned out to bags.
They informed Brisbane air traffic control and were asked to contact search and rescue via satellite phone.
"They wanted to call us but we did not know the number of the airplane so were able to contact our dispatch at Toronto on the satellite phone and have him phone Australian search and rescue," he said. "So they patched us through that way and one of the pilots gave them all the details."
Capt Robertson, who is Air Canada's fifth most senior pilot and has been with the company since 1973, said this was the first time he had been involved in this kind of event.
He said the exercise added about 40 minutes to the flight, which was already late because it had been diverting around weather near Hawaii.
"If we had been 40 minutes earlier, we would have been on the ground," he said.
After 16 hours drifting at sea, the yachtsman is in good spirits as he heads back to Sydney without his boat.
The 44-year-old lone yachtsman was recovered about 270 nautical miles off the coast of Sydney early today by NSW Water Police.
He's expected to be back on land by tonight.
An Australian Maritime Safety Authority (AMSA) spokeswoman said the sailor didn't have any injuries and was in "good spirits".
"He may receive medical assistance when he arrives at port, but that is up to police," she told AAP.
The AMSA spokeswoman said the yacht - which had a snapped mast - was either too damaged to be brought back to land or the weather conditions did not allow it.
She said the rescue highlighted the importance of having a distress beacon fitted with a GPS, which enabled authorities to locate boats within seconds rather than hours.