Predictably, the forward who scored a record 14 goals for Tottenham in the north London derby, was booed every time he touched the ball although the England captain was hardly involved in the early exchanges.
Bayern, whose disappointing season now rests on trying to win the competition for a seventh time, initially looked comfortable despite having no fans inside the Emirates as punishment for crowd trouble in the previous round.
But they were undone in the 12th minute when Ben White played the ball inside to Saka who had time to pick his spot and curl a low left-footed shot beyond Manuel Neuer.
White should have made it 2-0 soon afterwards but shot straight at Neuer and it proved costly as Arsenal's defence, so impregnable in the Premier League of late, went missing.
They carelessly lost possession in the 18th minute and Bayern punished them as Leon Goretzka slipped a perfect pass to Gnabry who clipped a finish past the on-rushing David Raya.
All Arsenal's poise vanished then as Sane was allowed to run and run before being tripped in the area by William Saliba and referee Glenn Nyberg had the simplest decision to point to the penalty spot.
Up stepped Kane, and despite the whistles no one really expected him to miss as he coolly sent Raya the wrong way.
With the 60,000 crowd suddenly having painful flashbacks of heavy European defeats by Bayern, notably a 10-2 aggregate defeat in 2017, it could have got worse as Sane burst through on goal and was only denied by a superb covering tackle by White.
Bayern displayed their European experience in the second half as they soaked up some Arsenal pressure while looking dangerous on the counter-attack.
With Arsenal struggling to create any meaningful chances Arteta sent on Trossard and Gabriel Jesus just past the midway point of the second half. And it was Trossard who brought the home fans back to life as he guided in a 76th-minute equaliser.
Bayern substitute Kingsley Coman almost won it for the visitors near the end with a close-range flick that hit the post while Arsenal were screaming for a penalty with the last action of the game as Saka went down in the area.