The puppy was due to fly from Nova Scotia on Wednesday to stay with family in Newfoundland, but landed in Ontario.
On arrival, flight staff took Cooper outside to relieve himself, but he slipped off his lead and escaped.
His owner, who was due to travel to Jamaica for a wedding, said on Friday she was "grateful" for his return.
The golden labradoodle was supposed to board a WestJet flight from Halifax on Wednesday bound for Deer Lake, but was placed on a plane destined for Hamilton, a city more than 2,000 km (1,200 miles) away.
"I got a call saying they had put my dog on the wrong flight to a totally different province," Cooper's owner, Terri Pittman, said.
On hearing the news, Ms Pittman took a flight to Hamilton, where she was joined by "thousands" of members of the public in the search for Cooper.
He was found wet and hungry on Friday by a group of local residents, CBC news reports.
"Knowing that people were spotting him running in the same area gave me more hope," Ms Pittman told CBC.
"The community of Mount Hope and Hamilton have been amazing," she said earlier, adding that "random people messaged me saying they want to help".
When Ms Pittman was informed by airline staff that Cooper had taken the wrong flight and had escaped, she said it was "one of the worst days of my life".
In a post on Facebook, Ms Pittman said: "This dog is everything to me, and the thought of losing him for good was sickening. To the city of Hamilton, I am overwhelmed."
Coincidentally Deer Lake, where Cooper was supposed to touchdown, is a town situated in the Canadian province of Newfoundland and Labrador.

Morocco start their Group C campaign against DR Congo on Monday, then face Togo on 20 January and take on Ivory Coast four days later.
Rherras, 23, and Cameroon midfielder Arnaud Djoum, 27, will miss Hearts' Scottish Cup meeting with Raith Rovers on 22 January.
Cameroon are in Group A with Burkina Faso, Guinea-Bissau and hosts Gabon.
Djoum has five international caps while Rherras made his Morocco debut in August.
Scottish Premiership clubs are currently on their winter break and Hearts' next league fixture is away to Celtic on 29 January.

The 35-year-old former international stand-off becomes the first French coach of the Perpignan-based club.
Frayssinous replaces Trent Robinson, who has left France for a post at Sydney Roosters in Australia.
Frayssinous is five months the junior of the previous youngest Super League coach, Bradford's Francis Cummins.
Frayssinous had been part of the Dragons' coaching staff and played for them when they made their Super League bow with a 38-30 win against Wigan in 2006.
The former assistant coach of the France national team has signed a two-year deal, with the option of a third season.
A missing labradoodle named Cooper, which sparked a major hunt after boarding the wrong flight in Canada, has been reunited with his owner.
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Hearts left-back Faycal Rherras has been given a late call-up to Morocco's Africa Cup of Nations squad.
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Laurent Frayssinous has been appointed the head coach of Catalan Dragons on a two-year contract, and becomes the youngest team boss in Super League.