The joint bid won 134 votes (67 percent) out of the 203 entitled to vote with Morocco bagging 65 (33 percent) when voting took place in Moscow on Wednesday, a day ahead of the Russia World Cup 2018.
The 2026 World Cup will head to North America for the fourth time and will be the first with 48 teams taking part.
For Morocco, it was the fifth time it had bid for the hosting rights to the football World Cup, calling it "the dream of a nation".
Meanwhile, the US hosted the World Cup previously in 1994 while Mexico hosted it in 1970 and 1986. Canada has never hosted a men's World Cup but held the women's tournament in 2015.
Earlier, US Soccer President Carlos Cordeiro has said his bid would generate $14bn in revenue and make an $11bn profit for FIFA. The bid also expects record ticket and hospitality revenue.
Although it would be the first tournament to be hosted by three nations, the vast majority of games will be held in the US.
"We can focus on the game. We are ready made. Our cities are ready to host today," said John Kristick, executive director of the United Bid Committee.
Al Jazeera's Gabriel Elizondo, reporting from New York, said: "While the official name of the bid is United 2026, the three potential host nations are right now anything but united".
"US President Donald Trump has disparaged Mexicans and wants to build a wall along the US-Mexico border. And the US-Canadian relationship right now is rocky - with both sides threatening a trade war," he said.
Trump has also backed the tri-nation bid and his administration has given guarantees about trade, tax and other requirements demanded by FIFA.
In April, Trump caused controversy with a tweet that some interpreted as a threat. "It would be a shame if countries that we always support were to lobby against the US bid. Why should we be supporting these countries when they don't support us (including at the United Nations)?" he wrote.