Carr opened his Magpies account with a great strike 12 minutes into the second half to settle a dull match and leave Southampton head coach Steve Wigley still searching for a first victory.
Newcastle were the better side from the first to the last minute and only a brave piece of defending from midfielder David Prutton prevented Lee Bowyer opening the scoring as early as the eighth minute.
Patrick Kluivert and Craig Bellamy, playing out on the right wing, combined before Kluivert pulled the ball back for Bowyer, only for Prutton to deny the former Leeds man with a great last-gasp block tackle.
Resurgent Southampton winger Fabrice Fernandes had the home side's first sight on goal seven minutes later.
Fabrice Fernandes has shrugged off the threat of a possible jail term to recapture the best form of his career this season.
The French winger nearly capped his impressive start to the campaign with a goal with a great long-range volley which was stopped on the line by Shay Given.
Former Saints hero Alan Shearer arrived at the St. Mary's Stadium looking for his first win in the City since leaving for Blackburn 12 years ago.
The ex-England man should of made that dream a step closer to reality when he planted a free header wide of the post from six yards out from a Bowyer corner.
Prutton then went close with a long-range effort in the 19th minute before Newcastle defender Andy O'Brien reacted superbly to deny James Beattie a clear shot on goal soon after.
Beattie picked up the ball on the edge of the area after Anders Svensson had broke free on the right, but O'Brien somehow got in the way of his shot after the England striker's fancy footwork had fooled the rest of the Toon defence.
O'Brien looked to continue his goal laden start to the season in the 31st minute.
The Irishman, who has scored two goals already this term, could have had a third when he was picked out by an Olivier Bernard free-kick only to head wide with just Antti Niemi to beat.
Saints were given another let-off four minutes later when Jermaine Jenas somehow failed to connect to a ball when bearing down on Niemi after Kluivert had headed Bellamy's cross into his path.
But the home side's good fortune ran out on the stroke of half-time when Prutton turned the ball into his own net.
Bellamy, clearly enjoying himself on the wing, picked out Shearer at the back post with a pinpoint cross and the Newcastle captain drilled a hopeful shot goalwards which Prutton turned past Niemi from two yards out.
Anders Svenssonn drew Southampton level with his second goal of the season eight minutes into the second half.
Rory Delap's long throw was only half cleared and Svensson brilliantly streered the ball into the bottom left-hand corner of the net after Prutton's shot had rebounded into his path.
However, Saints' joys was short-lived as Carr won the game for Newcastle four minutes later.
The Republic of Ireland full-back fired in a fantastic 30-yard piledriver which flew past Niemi and into the far corner of the net to seal victory.