Substitute Alex Oxlade-Chamberlain had looked to have put the visitors on course for victory with a 70th minute solo strike, but the sensational finale means Gareth Southgate's men will be delighted to have come away with a point.
The result sees the Three Lions remain top of Group F after six games played, but their lead was sliced to two points following Slovakia's triumph in Lithuania later on Saturday.
Scotland are currently fourth on eight points, and will feel their hopes of pushing for the runner-up spot and a potential play-off berth were cruelly dented by Kane's late intervention.
Gareth Southgate, Harry Kane
Image credit: Getty Images
Harry Kane is still trying to replicate his Spurs form for England - but that goal and the captaincy could be the key. The Spurs hitman has won the past two Premier League Golden Boot awards and finished the season on fire - but he has yet to truly ignite with his country. The 23-year-old has now netted six times in 18 appearances for the Three Lions, but it looked like being another one of those days when he wasted two first-half chances he would have gobbled up in his sleep in his Lilywhites shirt.
History has shown some players just can't recreate their exploits for their club on the international stage, but Kane is unlikely to fall into that bracket and his late strike to save the day may be a significant sign post and see him appointed captain on a permanent basis.
MAN OF THE MATCH
Leigh Griffiths (Scotland): The Celtic man was starved of service throughout but worked tirelessly and looked to have won it with two sensational free kicks late on - his first goals in 13 caps for Scotland.
Scotland: Gordon 6, Tierney 7, Berra 6, Mulgrew 7, Robertson 7, Brown 6, Morrison 5, Snodgrass 6, Armstrong 6, Anya 6, Griffiths 8. Subs: McArthur 6, Fraser 6, Martin n/a.
18' - ENGLAND CHANCE! Dier picks out Kane with a chipped ball into the box, but the England skipper can only rifle over the top after taking it down well and cutting back onto his left foot.
22' - ENGLAND CHANCE! Lallana wriggles free close to the left byline and somehow digs out a lovely cutback for Kane who completely miscues from six yards out.
51' - ENGLAND HIT THE POST! Livermore cross from the right takes a wicked deflection off a defender and comes back off the near post.
70'- GOAL! Scotland 0-1 England. Oxlade Chamberlain makes an instant impact! The Arsenal man jinks in from the right and squeezes a shot through a swarm of bodies and into the net via big hands from Gordon.
87'- GOAL! Scotland 1-1 England. Griffiths steps up and curls a stunning 25-yard free kick beyond Hart and into the far corner of the net.
90'- GOAL! Scotland 2-1 England. Incredible scenes as curves another sublime free kick over the wall and into the opposite corner. Lightning strikes twice!
90+3' - GOAL! Scotland 2-2 England. Kane levels for the Three Lions! Sterling rakes a ball from the left to the far post where Kane arrives to volley home.
Kane - Scotland-England
Image credit: Getty Images
Alex Oxlade-Chamberlain scored his first England goal since October 2015 vs Lithuania - 607 days ago
England are unbeaten in their last five visits to Scotland.
Scotland are unbeaten in their last six home games.
Griffiths scored his first international goals on his 13th cap. They were also the first goals England have conceded in this World Cup qualifying campaign
Kane scored his first goal for England since May 2016, after a run of 575 minutes without one.