The six-foot-11-inch, 240-pound Villanueva was a second-team Big East all-star last season, leading the conference in rebounding. He was also a member of the 2004 NCAA-champion Connecticut squad.
However, the selection was universally panned by ESPN's basketball analysts during the live TV broadcast since Villanueva was projected by most experts to be taken much lower in the draft.
The pick also drew boos from a crowd of Raptors season-ticket holders gathered at Toronto's Air Canada Centre.
Charlie Villanueva, right, a forward from Connecticut, is congratulated by NBA commissioner David Stern after being chosen by the Toronto Raptors at the NBA Draft on Tuesday. (AP Photo/Kathy Willens)
"I can't worry about the crowd," Raptors general manager Rob Babcock told Raptors TV.
"He's a good rebounder and he's an improving player, he's only 20 years old," added Babcock. "He's a young player who has shown a learning curve that he is improving on."
While Villanueva has earned a reputation as an excellent rebounder and ball distributor, some have questioned his drive and work ethic while at Connecticut.
Villanueva is also a power forward – the same position played by the Raptors' budding franchise cornerstone Chris Bosh.
Babcock earned better reviews later in the evening for his second first-round selection, choosing forward Joey Graham from Oklahoma State 16th overall.
"Joey Graham gives us toughness, he gives us defence, and he gives us 100 per cent effort," said Babcock.
The Raptors then took a pair of Europeans with two second-round choices. Toronto selected 21-year-old Croatian guard Roko-Leni Ukic 41st overall and Italian League forward Uros Slokar, 22, of Slovenia with the 58th pick.
But the story of the night for the Raptors was the surprising No. 7 Villanueva pick.
"That pick makes no sense whatsoever ... when you think about the fact this team got hoodwinked when they traded away Vince Carter virtually for nothing," ESPN analyst Steven A. Smith said of the pick.
"We sit here today wondering what on earth Rob Babcock is thinking. What is he doing?"
It marks the second straight year Babcock has confounded NBA analysts and fans with an unconventional early first-round pick.
Babcock picked centre Rafael Araujo eighth overall in the 2004 NBA Draft. The Brazilian big man struggled last season during his rookie campaign.
The Raptors GM went the more predictable route with his Graham pick. The six-foot-seven-inch small forward was MVP of the 2005 Big 12 conference tournament.
Scouting reports list Graham as one of the best athletes in the draft. He is also touted as a solid defender and high-percentage shooter.
The Raptors received the 16th pick used to take Graham as part of the blockbuster swap that sent Carter to the New Jersey Nets on Dec. 17, 2004.
Bucks pick Bogut first overall
As anticipated, the Milwaukee Bucks used its first overall pick to take Australian centre Andrew Bogut. The seven-foot, 245-pound sophomore from the University of Utah was named the 2004-05 U.S. college player of the year.
"It's one of the best days of my life, and my family's," Bogut said. "I am going to be a workhorse."
Bogut, 20, is the first American collegiate player taken with the top pick in the NBA Draft since the New Jersey Nets selected Kenyon Martin out of Cincinnati in 2000.
Since then, three high school players – Kwame Brown (2001), LeBron James (2003) and Dwight Howard (2004) – along with Chinese centre Yao Ming (2002), were selected with the top pick.
After the Bogut pick, the Atlanta Hawks selected Marvin Williams, a forward from the University of North Carolina, with the second overall selection.
The Utah Jazz took guard Deron Williams out of the University of Illinois with the third selection.
Guards also went fourth and fifth overall. The New Orleans picked Chris Paul of Wake Forest with the No. 4 selection, while the Charlotte Bobcats opted for Raymond Felton of the University of North Carolina with the fifth choice.
The Portland Trail Blazers used the sixth overall pick to select 18-year-old Martell Webster – the first high school player taken on the night. Toronto then selected Villanueva.
with files from Canadian Press