The All Blacks suffered a double injury blow in the opening half of the Lions series, with Ben Smith and Ryan Crotty both forced from the field.
Smith was substituted in the 26th minute after sustaining a blow to the head, while Crotty joined him on the sidelines after appearing to strain his hamstring in the 33rd minute.
Both players have suffered similar problems in the past and the pair's involvement in the rest of the series must now be in doubt.
Smith was sidelined for two weeks earlier in the Super Rugby season after sustaining a concussion while playing for the Highlanders. It was the fullback's fourth concussion in the past five years.
While little is yet known on the severity of Smith's current problem, the fact he was unable to return will leave the All Blacks taking a cautious approach with regard to their vice captain's health.