The Black Cats appeared to be moving to within four points of the Champions League places after Asamoah Gyan's ninth goal of the season put them 2-1 up early in the second half.
But Huth claimed an equaliser seven minutes from time after John Carew had cancelled out Kieran Richardson's second-minute opener just after the half-hour, and the German then slid home the winner in stoppage time to stun the visitors.
The first two goals would have left Black Cats boss Steve Bruce fuming as the first looked offside and the second appeared to reach Huth via the arm of Norway international Carew, brought in from Aston Villa last month.
But all would have frustrated the former Manchester United centre-back as they all came from set-pieces which were not well defended.
On a windy day at The Brit, Sunderland found themselves under something of an aerial bombardment from corners and Rory Delap's long throws.
But until late on they appeared to have weathered the storm, having taken the few chances they had better than their opponents.
And they could not have got off to a better start, taking the lead after just one minute and 52 seconds through the in-form Richardson.
Sunderland striker Gyan's wild thrash at the ball inside the penalty area fortuitously dropped to the midfielder and he hammered home left-footed his fourth goal in his last three matches.
Stoke came close to equalising almost immediately as Etherington's corner dropped to Huth at the far post.
The centre-back's first shot bounced back off the chest of goalkeeper Craig Gordon but he wastefully ballooned over the second from close range.
It signalled a sustained spell of pressure for the Potters, with Nedum Onuoha deflecting wide a Jermaine Pennant shot from the edge of the area and Danny Higginbotham hooking into the side-netting at the far post.
The gusty wind was undoubtedly helping Delap's throw create uncertainty in the Sunderland penalty area and one such set-piece let to Stoke's equaliser, for which Craig Gordon had to take some of the blame.
Delap's 32nd-minute delivery was headed up in the air and as the goalkeeper came to claim he was beaten to the ball by Huth, who was able to nod on via Gordon for Carew to stab home from a yard out for his first in four appearances for his new club.
Debate raged over its legitimacy as Carew was in an offside position but there was an element of doubt as to whether the ball had actually come off Gordon.
It quickly subsided three minutes after the break as Sunderland went ahead for the second time.
Etherington ran into trouble 15 yards into Sunderland's half and Black Cats debutant Sulley Muntari, on loan from Inter Milan, quickly launched the ball forward, catching Huth exposed to a one-one-one with Gyan.
The Stoke centre-back got himself in a complete tangle in the penalty area, allowing the Ghana international to cut back inside and fire past Asmir Begovic for his ninth goal of the season.
Long throws still continued to provide a threat, however, and from one Shawcross' shot was blocked by a packed defence with Delap's fierce strike flattening Phil Bardsley as he headed behind.
But just when it seemed their aerial assault had run its course Stoke struck again seven minutes from time.
It was a scrappy effort but when Pennant curled in a free-kick from the left, Carew's determination got him to the ball before Gordon and he bundled the ball goalwards, with Huth getting the final touch.
Sunderland looked like they were hanging on and, criminally, they cracked again in the third minute of injury time.
Pennant's inswinging delivery from the left again caused problems and Huth slid in from close range to stab the ball past Gordon.