Spurs moved to sign the 25-year-old Danish international when he informed Southampton that he would not extend his current deal.
Tottenham said on their official site: "The midfielder has a signed a contract with the Club until 2025 and will wear the number five shirt."
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Financial details of the transfer were not disclosed but British media reported that Spurs have paid Southampton around 15 million pounds ($19.64 million) to sign the 25-year-old Hojbjerg who had a year left on his contract.
Hojbjerg made 134 appearances for Southampton in all competitions after joining the south-coast club from Bundesliga side Bayern Munich in 2016.
"What was very important for me is that I wanted to play in a club where I could see myself for many years," Hojbjerg said in a video posted on the Spurs Twitter account.
"Tottenham was just the one. I'm very proud... I think there's a fantastic future ahead for the club. And I wanted so much to be a part of that."
The player becomes Spurs' first signing of the summer transfer window, and could replace Tanguy Ndombele, who has failed to establish himself in the first team under Jose Mourinho following his move from Lyon in 2019.
At the same time the clubs confirmed that Kyle Walker-Peters had moved permanently to St Mary's after spending the last half of the season on loan from Spurs.
"It was not easy for Kyle when he arrived here. He needed some time to adapt to our style of play, and then we had this period where we could not be together as a team," Southampton boss Ralph Hasenhuttl said in a statement.
"But you could see from how he performed when we came back that he had worked a lot in this time, both on his physical condition and also on his understanding of our own game. It says a lot to me about this player that he was able to do this.
"He's a good fit for our style."
Additional reporting from Reuters
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