But Welbeck was on hand to score a second of the afternoon and secure a 3-2 win for Arsenal - who have won six games in a row for the first time this season - as a fiery end to the game saw both sides finish with 10 men as Jack Stephens and Mohamed Elneny saw red.
The Frenchman has been a revelation since coming to England, successful the league title in two consecutive years with totally different groups.
But Pierre-Emerick Aubameyang and Welbeck orchestrated a first half comeback with well-taken goals to offer some evidence that Arsenal's players haven't given up on the league just yet.
Shane Long snuck in between Petr Cech and Shkodran Mustafi to tap home from four yards out.
In the early exchanges of the second half, Southampton would have had McCarthy to thank for keeping them in the game, when he was forced into good saves from Aubameyang and Xhaka, before he pushed away a Iwobi shot. Long almost scored another, but he was flagged for offsides.
It was a game of great saves and very bad defending, of fine attacking play and gripping twists in the narrative, and there was a redemptive ending for the enduring frustration that is Danny Welbeck.
It looked like the Saints had snatched a point on 73 minutes when substitute Charlie Austin turned in Soares' cross with nearly his first touch of the game.
They took the lead nine minutes before the interval, after Cesar Azpilicueta found space at the back post to make it 1-0.
Arsene Wenger's men needed to respond and so they did.
Yet the speed with which it was replaced by despair encapsulates why their hold on their Premier League status remains so uncertain. Southampton's Jack Stephens and Arsenal's Mohamed Elneny were both sent off in the dying minutes.
It is just one win in 19 league matches now and they have conceded six goals in two league games since Hughes replaced the sacked Mauricio Pellegrino in the middle of March.
Antonio Conte's facet have picked up simply 12 factors of their 11 Premier League video games since New Years Day, dropping from second to fifth and now Arsenal are simply three factors behind.
"We conceded poor goals, that's the story of our season", Hughes said. Cedric Soares put the ball across the area and Charlie Austin has the easiest task in the world to tuck the ball into an empty net to make the scoreline 2 - 2.
Today he pulled his socks, figuratively and metaphorically, as he helped Arsenal pick up another three points at home with a rare start. "Clearly we were quite prepared to allow Arsenal a lot of possession in front of us, but our intention was to counter quickly and put Shane Long in areas high up the field where we could get support to him".