Xhaka almost conjured an equaliser with a dipping long-range effort that Dean Henderson pushed away at full stretch.
Mesut Ozil was once again left out of the Arsenal squad and, with Aubameyang anonymous, Emery sent on Dani Ceballos for Joe Willock at half-time for an injection of creativity.
The on-loan Real Madrid midfielder should have equalised when he shot weakly at Henderson from Saka’s cross.
Always creaky at the back, Arsenal were nearly caught when Fleck thudded into the side-netting and then forced Bernd Leno into an unconvincing save.
Alexandre Lacazette came on with 22 minutes left for his first appearance since suffering the ankle problem that had ruled the Arsenal striker out since the start of September.
For all their territorial dominance in the closing stages, Arsenal lacked composure in the final third.
Pepe curled just wide and Kolasinac headed over as the visitors’ frailties were laid bare.