Ziyech gave Morocco the lead as he converted a 29th-minute penalty and he delivered the inch-perfect cross for Khalid Boutaib to head the winner after Dusan Tadic had equalised.
The Serbians started in an adventurous formation with three forwards and two attacking midfielders, but the unfamiliar strategy left anchorman Nemanja Matic with too much work to do.
Toothless in attack, they looked shaky at the back whenever Morocco came forward and Ziyech made no mistake with the spot-kick after Nikola Maksimovic hauled down Nordin Amrabat.
Tadic, making his 50th international appearance, levelled with a crisp shot from eight metres with his weaker right foot in the 37th minute after a defence-splitting pass by Adem Ljajic left him with time and space.
The Moroccans were in front again three minutes later as Ziyech broke down the right and swung in a delightful cross for Boutaib, whose header gave goalkeeper Marko Dmitrovic no chance.
Filip Kostic and Aleksandar Mitrovic missed late chances for Serbia, who face Nigeria in another warm-up at Barnet's stadium in London on Tuesday.
(This story corrects Nemanja to Nikola in paragraph four.)
(Writing by Zoran Milosavljevic in Belgrade; Editing by Ian Chadband)
