The move worked early, with the Portuguese finding space down the left flank and linking well with Musiala in the centre.
Arsenal coach Mikel Arteta opted for the defensive stability of Takehiro Tomiyasu in place of Jakub Kiwior at left-back to neutralise Leroy Sane but the Japanese, who was making his first start since December, notably lacked rhythm.
Tomiyasu completely misjudged a Musiala pass early, allowing Sane to stroll through the Arsenal box and force a corner.
Gabriel Martinelli was the visitors’ most dangerous in the opening half. He scuffed a curling ball just wide of the post after seven minutes and then shot directly at Neuer with the goal beckoning on the half-hour mark.
Bayern were the better team after the break and went close immediately, Leon Goretzka heading a clever Kimmich cross onto the woodwork.
The pressure began to tell and Bayern broke through after 63 minutes when Kimmich, among the shortest players on the pitch, was allowed to slip through a crowded Arsenal box and head in a Guerreiro chip.
The hosts almost doubled up moments after when Kane found an unmarked Sane in the box, but the Germany winger blasted his shot skywards.
Arsenal pushed for an equaliser and went close in stoppage time when Kai Havertz and Bukayo Saka lashed at a bouncing ball in the box but could not break through, ending the visitors’ hopes of a return to the Champions League semis for the first time since 2009.
