The 24-year-old Wallaby had been eyeing a spot in the squad to face the touring Lions in June, calling it a "huge occasion".
He managed only 32 minutes on the pitch, though, throwing himself into contact against a hugely physical Tongan side only to limp to the sidelines just before half-time clutching his hamstring.
Brumbies coach Jake White will now wait for results of scans before making a final call on McCabe's availability.
"I'm not going to risk him now because I don't want him breaking down and then it goes the whole season," said White.
"It's tough for him it's a freak thing because this injury has nothing to do with his neck. He's been training hard and well.
"It's not a major thing; it was just one of those things."
Known and respected for his bravery and highly physical playing style, McCabe is a key feature in the Brumbies and Wallabies line-ups and is also a member of the five-man leadership group within the national side.