Gnabry, deemed not good enough for English football after spells at the Gunners and West Brom, produced a quartet of clinical finishes after the break to send the German champions soaring clear at the top of Group B.
Bayern are supposed to be a team in transition but they ripped Tottenham apart in the second half and look real contenders for this competition.
It leaves the Premier League side in an all-too familiar position of floundering in the early part of the group stage, having had to perform a miracle to progress to the knockout stages last year.
This hammering, the worst under Mauricio Pochettino, will lead to some inquest, and they already have work to do if their Champions League journey is not going to end before Christmas.
It seems impossible to think that Spurs – after a pulsating opening – actually took a 12th-minute lead as Son eventually made it third time lucky having twice being denied by Manuel Neuer.
Their high-energy press paid dividends as Dele Alli won the ball, which allowed Moussa Sissoko to play Son in and this time he buried a low shot past Neuer and into the bottom corner.
It was Son’s first goal against Bayern after fruitless spells in Germany for Bayer Leverkusen and Hamburg.
But just 194 seconds later the Germans were back level with a goal out of the blue.
They got in behind Spurs down the right and the ball ended up with Kimmich 20 yards out and his curling strike was too good for the outstretched hand of Hugo Lloris.
The efforts that rained in on goal at both ends were almost as torrential as the north London weather and the best of them fell to Tottenham.
Kane almost took advantage of some Kamikaze goalkeeping from Neuer, who raced off his line, but after rounding the keeper, the England captain saw his shot blocked on the line by Jerome Boateng.
Then a fast-paced incisive move deserved a goal as Kane brilliantly switched play to Serge Aurier whose cut-back was perfect for Ndombele, but the Frenchman’s shot was to close to Neuer and the German pulled off a smart low stop.
That was as good as it got for Spurs, as Bayern ran riot.
They enjoyed their best spell of the half in the final minutes before half-time and it saw them take the lead.
Some sublime skill by Lewandowski saw him breeze into the area and after Spurs failed to clear, the Poland striker clinically fired a low shot-on-the-turn into the bottom corner.
Bayern ran clear with two goals in two minutes after the restart as Gnabry enjoyed his north London return.
First he was allowed far too much room to advance down the left, cutting inside to drill a fine finish into the bottom corner and moments later, after Harry Winks was robbed of possession, he found the other one after Corentin Tolisso’s assist.
Spurs briefly threatened a comeback as Kane slotted home a penalty after Kingsley Coman’s foul on Danny Rose and then Sissoko and Christian Eriksen missed good chances.
But Bayern were in the mood to leave their hosts red-faced and they produced a devastating final 10 minutes.
Gnabry claimed the matchball when he raced clear and slotted home, before Lewandowski found the bottom corner in the style expected of him.
German international Gnabry then completed his night to remember when he struck a fourth to leave Tottenham shell-shocked.