The 30-year-old, who was due to be a free agent in the summer, has agreed terms on a three-and-a-half-year deal at the north London club.
Alderweireld looked set to be leaving Spurs at the end of the current campaign as negotiations over a new deal had stalled and under Mauricio Pochettino there appeared to be little chance of them restarting.
But the arrival of Jose Mourinho has brought about a change and the Belgium international will now stay until 2023.
A club statement read: “We are delighted to announce that Toby Alderweireld has signed a new contract with the club until 2023.”
Despite his contract stalemate Alderweireld, who followed Pochettino to Spurs having been on loan at Southampton in 2015, has been a mainstay of the defence in recent times, making 50 appearances last season.
The club exercised an extension in his contract last term which also triggered a £25million release clause, but only Roma were interested in the centre-back and made a much smaller bid in the summer.
Alderweireld, who has a young child and a second on the way, has now decided to stay in London and has committed his long-term future to the club.
Alderweireld’s Belgium team-mate Jan Vertonghen is also out of contract in the summer and can discuss terms with European clubs in the new year, though has expressed a desire to sign a new deal.
Christian Eriksen has reportedly told Mourinho he will not sign a new contract and looks set to leave on a free in the summer, unless Spurs can sell him in January.