Winks suffered the injury in Saturday's 2-0 victory at Burnley and received oxygen on the side of the Turf Moor pitch before being stretchered off.
Mauricio Pochettino claimed yesterday that it was unlikely the midfielder would be able to return to fitness during the run-in and the Argentine coach's fears have now been confirmed.
A Spurs statement read: "We can confirm that Harry Winks sustained ligament damage to his left ankle during Saturday's win at Burnley.
"Harry Winks will continue to be monitored by our medical team during his recovery and will be unavailable for the remainder of the season."
Winks, who signed a new five-year deal at White Hart Lane in February, struggled for game time last season but has developed into a serious option this term, making 33 senior appearances.
The England Under-21 international, whom Standard Sport understands is on the cusp of a senior call-up after impressing Gareth Southgate, is rated highly by Pochettino.
Suffering such a serious injury after breaking into the team will undoubtedly test the youngster's character but Pochettino is adamant Winks must use the experience positively.
"(In adversity) you build your character, your personality, strong belief and mentality.
"It’s a negative thing but you can turn that into something positive, and come back stronger than before. It's all about learning.
"You should always be positive and we’ll help him to be positive with good energy to be available as soon as possible," Pochettino told Tottenham's official website.
Erik Lamela (hip) has also been ruled out for the rest of the season while Harry Kane (ankle) and Danny Rose (knee) are fighting to return during the run-in.
Victor Wanyama is a doubt for tomorrow's trip to Swansea, having picked up a back problem against Burnley, which could pave the way for Mousa Dembele and Eric Dier to be paired in midfield.