Aguilar had suffered a forearm fracture in August during the Europa League qualification against Pafos and only made his comeback at the beginning of September.
Veratschnig and Redzic Also Out
Furthermore, captain Nikolas Veratschnig sustained a ligament injury in his right knee during his senior national team debut for Austria against Kosovo.
The 23-year-old has returned to Salzburg and will be "unavailable for several weeks".
Damir Redzic has been back in Salzburg since yesterday, Monday. The Hungarian had to be substituted during his country's Nations League clash with Ukraine after a rough challenge.
He suffered a ligament injury in his right ankle and will also be unavailable for a few weeks.