Southgate limped out of training on Tuesday with a knee problem, which could see him miss the rest of the season.
Boro are still hopeful that scans will show there is nothing serious wrong with their skipper, but they have now recalled Cooper.
The 37-year-old was set to play for The Black Cats in their game at Wimbledon on Tuesday evening - but Boro insisted he returned before the match.
Cooper, who is in talks with Boro about prolonging his stay, will provide back-up to Chris Riggott and Ugo Ehiogu as the Teessiders are now growing short on defensive options with youngster Andrew Davies also sidelined with a fractured leg.
Meanwhile, Boro have allowed young full back David Murphy to stay on loan at Barnsley until the end of the season.
