Sexton, who moved to Racing in the summer following three Heineken Cup crowns with Leinster, started the 32-15 reverse to the Wallabies in Dublin but failed to reappear for the second half after leaving the field in some discomfort after the first 40 minutes.
"Jonny has a hamstring injury, we're just not sure of the extent of the injury at the moment," said Ireland head coach Joe Schmidt, who was Sexton's provincial boss for two of his Heineken Cup winning seasons.
"To be honest it's too early to tell. He felt it wasn't particularly bad and he pulled up quickly. But it's out of our control, we just have to wait and see what happens and wait for the results of the scans. We'd given Jonny a weekend off and a refresher and we thought we'd get two big weeks out of him, so it's really disappointing."
Sexton had been rested for the 40-9 win over Samoa just over a week ago but will now almost certainly miss Ireland's clash with the All Blacks on Saturday. Of more concern for Racing is Sexton's availability for their Top 14 ties with ASM Clermont Auvergne and Montpellier and their huge Heineken Cup double header with Harlequins.
Racing have started their Heineken Cup campaign with a win and a draw to occupy joint top spot in Pool 4 and back-to-back victories over bottom-placed Quins would put them on the front foot as they look to secure a first quarter final.
Having seen off Clermont in Round One and then shared the spoils with the Scarlets in Llanelli, Racing take on the former Amlin Challenge Cup winners at the Stade Yves du Manoir on Saturday, December 7, before heading to London the following Sunday.