Bowden took a heavy knock late in the Highlanders' 17-47 loss to the Bulls in Pretoria on Sunday and it was later discovered he had concussion.
He will be stood down from rugby for two weeks, leaving the Highlanders with just one specialist first five, Mike Delany, and utility back James Wilson, who has started the last three games in the No 10 jersey.
‘‘It is unfortunate for Dan to be leaving us but head injuries have to be treated with caution and we have decided it would be best for him to go home to rest and recover,'' Highlanders coach Glenn Moore said.
Many considered the steady Stewart to be unlucky to miss selection for the Highlanders.
He has been training with the wider squad and playing club rugby in Invercargill.
The Otago Daily Times understands Glen Horton was also on standby to join the Highlanders, with fullback Paul Williams initially under some sort of injury cloud.
Both Williams and No 8 Steven Setephano (shoulder) appear likely to be available to play the Stormers in Cape Town this weekend.
The Stormers have their own injury problems, with winger Tonderai Chavhanga (hamstring) out for a month and prop JD Moller (shoulder) gone for several months.
