Jonas Hofmann put the Germans ahead after 50 minutes but the visitors were awarded a penalty in the final five minutes.
After a long VAR check, Nico Schlotterbeck was adjudged to have brought down Kane in the area and Kane equalised from the spot to claim his 50th international goal.
The result means that England came away with one point from their opening two Nations League games after defeat to Hungary on the weekend.
After suffering a first defeat by Hungary for 60 years on Saturday in their opening League A, Group Three fixture, England fielded an experienced lineup in a noisy Allianz Arena but were second best for much of the clash.
Borussia Monchengladbach midfielder Hofmann had the ball in the England net early on as Germany dominated but an offside flag cut short his celebrations.
He was not to be denied though and he beat Jordan Pickford with a powerful, slightly-deflected shot from the edge of the penalty area five minutes after the interval.
Despite a rather laboured performance, England had their chances with Bukayo Saka inches away in first-half stoppage time and Mason Mount and Kane both denied by Germany keeper Manuel Neuer as England sought a leveller.
"It is really important to show the mentality, 1-0 behind we showed good character to get back into the game and get a result," Kane, who is now three goals behind England's all-time top scorer Wayne Rooney, said.
"We were playing against a very good Germany side. We kept going and played our best football in the last half an hour."
It was a frustrating end to the game for Germany who have drawn both their opening matches in the group. England, who face group leaders Italy at the weekend, are bottom.
Germany were far sharper for most of the evening and thought they had gone ahead midway through the first half when Hofmann galloped clear and beat Pickford, but a VAR check confirmed that the offside decision against him was correct.
Stuttgart-born teenager Jamal Musiala, who grew up in London, was a thorn in England's side down the left and was involved in much of the home's side good work.
Germany did get ahead after a neat build-up saw Joshua Kimmich play the ball in to Hofmann who was allowed to turn too easily to fire a shot that Pickford got a strong hand to but could not prevent from going into the net.
But England rallied and when Kane broke into the box on to Jack Grealish's pass he was clipped by a stumbling Schlotterbeck and the Spanish referee awarded a penalty after checking a pitch-side monitor.
Kane then sent Neuer the wrong way to at least give England something to take home, although manager Gareth Southgate will have plenty to ponder.
Information from Reuters was included in this report.