Having already posted one 1-0 defeat from their opening battle with Hungary, England were staring down the barrel of a second consecutive loss amid a disappointing start to the contest.
Gareth Southgate's side got to half time with the scores level before Jonas Hofmann fired home the opener on the 50-minute mark, but England were handed a chance to restore parity in the dying embers.
Germany defender Nico Schlotterbeck lost his balance and bundled over Kane inside the area, although the Tottenham man was seemingly in an offside position before replays showed the last touch had come off a Mannschaft defender.
Referee Carlos del Cerro Grande awarded England the spot kick after checking the pitchside monitor, and Kane sent Manuel Neuer the wrong way to rack up a half-century of goals for his nation.
The 28-year-old has now become England's outright second-highest goalscorer - surpassing Sir Bobby Charlton's 49 - and he is only four away from breaking Wayne Rooney's all-time record of 53.
England's point against Germany still leaves them bottom of League A Group C ahead of Saturday's Euro 2020 final repeat with Italy at Wembley.