The 20-year-old Welshman featured from the start in Saturday afternoon's victory over the Cheetahs in Bloemfontein but has since been told by medical staff that he faces up to a month on the sidelines and will therefore not be able to play any further part in the tour.
The Cardiff Blues wing has spoken of his huge disappointment at being forced out of the remaining seven matches but he has also vowed not to dwell on the frustration and will instead throw himself fully into his rehabilitation.
"Obviously I am gutted to have this happen a second time, but understand that it is just one of those things, sport is like that," said Halfpenny, who made his international debut just seven months ago during the autumn internationals.
"It's frustrating but I just need to get on with the rehab, have some down time and get fit mentally and physically for the start of the new season.
"It's been an amazing experience being involved as I have been with the 2009 Lions, the team spirit is fantastic. It's just a great shame that I couldn't see it to the end but I wish the lads well for the build up to the Tests."
The Lions face the Sharks in Durban this evening (kick-off 6.10pm UK time) with Halfpenny's spot among the replacements having been taken by fellow Welshman James Hook.