Cowan was replaced early in the second half after making a lunge at the try line which resulted in a dislocated finger on his right hand. He is expected to return for the Highlanders' round six match against the Sharks in Dunedin on March 20.
Scott Cowan, who is part of the Highlanders wider training squad, will fly to South Africa as replacement for his brother.
Jamie Macintosh will captain the Highlanders for their final match in South Africa against the Bulls on Sunday morning (NZT).
