Vargas had provided the assist for Dimi Petratos' 44th minute winner in the 2-1 victory away to Roar.
The Venezuelan forward had to be replaced after 64 minutes after a nasty clash with Brisbane Roar's Matt McKay.
Vargas' left ankle appeared to buckle upon contact with McKay, with the 30-year-old immediately indicating the injury was serious.
The Jets confirmed after the game that Vargas had been taken to hospital for scans on a "very serious ankle injury".
A shattered Jets coach Ernie Merrick said: "The win means nothing really."
Merrick added: "Any player suffering an injury like that (hurts). He was loving life in Newcastle, big move for him, but he'll be with the surgeon tonight."