The Gunners edged in front through their only on-target attempt of the first half as Xhaka's swerving shot somehow got the better of a wrong-footed David de Gea.
Romelu Lukaku missed a couple of good chances either side of that strike, which would ultimately come back to haunt United thanks to Aubameyang's successfully-converted penalty after Fred shoved Alexander Lacazette in the box.
Relive how the 90 minutes of action unfolded with Sports Mole's live text coverage below.
Arsenal have won two of their last three Premier League home games against Man United, as many as they had in their previous eight against them, but the visitors were victorious here in January's FA Cup fourth-round tie.
STARTING XI: Leno; Sokratis, Koscielny, Monreal; Maitland-Niles, Ramsey, Xhaka, Kolasinac; Ozil; Lacazette, Aubameyang
SUBS: Cech, Mustafi, Elneny, Guendouzi, Suarez, Iwobi, Nketiah
STARTING XI: De Gea; Young, Smalling, Lindelof, Shaw; Dalot, Fred, Matic, Pogba; Lukaku, Rashford
SUBS: Romero, Bailly, Rojo, McTominay, Pereira, Martial, Greenwood