Bowe, meanwhile, lined up against O'Brien in that match but he too has seen his season interrupted by injuries.
And Schmidt believes that both would be better served with a rest rather than a trip to face the Pumas.
"It's really just player management," Schmidt said.
"There are guys who have had continuous niggly injuries that are going to be given a good amount of time in the pre-season to recover from those.
"Obviously Sean (O'Brien) has come back (after shoulder surgery) and played very few minutes.
"It was a discussion I had with both players (O'Brien and Bowe), and there are a number of others who we would feel are better served by getting a window to fully recover.
"Also a number of them have accumulated very brief pre-seasons by the time they go away on June tours, Lions tours and the like."