The 21-year-old was returning from more than a month on the sidelines with liver and hamstring injuries and, playing at fly-half, showed glimpses of why many consider him one of the most dangerous backs in rugby.
His involvement came to an end early in the second half, however, with the injury ruling him out of the Rebels' touring party for their last two matches of the season in South Africa.
O'Connor faces up to two months on the sidelines and must be considered a doubt for Australia's first match of the Rugby Championship against world champions New Zealand in Sydney on August 18.
Fellow Rebel Kurtley Beale also took a knock in last Friday's defeat to the Queensland Reds and missed Sunday's flight to South Africa.
The versatile back, who missed the first two of Australia's three wins over Wales in June, would be assessed by medical staff on Tuesday before a decision was made on whether he joined the Rebels in South Africa, the team said in a release.
The Rugby Championship replaces the Tri-Nations with Argentina joining Australia, New Zealand and South Africa for the first time in the southern hemisphere's annual international championship.