A fee reported to be in the region of $A3.1 million has been agreed for the 20-year-old, who will add to Wenger's defensive options.
But the Frenchman sees the Greece Under-21 international as a long-term prospect, with Mavropanos set to be sent out on loan.
"Yes, but he's not ready to play," Wenger said of Mavropanos' impending arrival following Wednesday's 2-2 Premier League draw with Chelsea.
"He will go out on loan."
Mavropanos will be the first Arsenal signing since the overhaul of the club's scouting and recruitment department.
Head of recruitment Sven Mislintat was brought in from Borussia Dortmund in November to take over from long-serving chief scout Steve Rowley.