The move reunites the hard-tackling Kenyan with former Southampton manager Mauricio Pochettino, the Argentine who took over at White Hart Lane in May 2014, as Spurs' first signing of the close season.
No financial details were given by the club, who secured a place in the Champions League by finishing third last season, but British media put the deal at 11 million pounds.
"The mid fielder has agreed a contract with the Club until 2021," Spurs said on their website (www.tottenhamhotspur.com).
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The Kenya international, who turns 25 on Saturday, helped Southampton to sixth place last season under Ronald Koeman, who has since taken over as Everton manager.
Wanyama had asked to leave last year after Tottenham first expressed an interest, but stayed on at St Mary's.
(Reporting by Alan Baldwin, editing by Ian Chadband)
