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Southampton took the lead on 35 minutes through Ross Stewart, but Arsenal was level midway through the second half when Viktor Gyokeres equalised. The Premier League leader looked the most likely winner from there.

But when the home side launched a counter-attack on 85 minutes, it did so with numbers and Tom Fellows fed Charles in the box for him to poke the ball past goalkeeper Kepa Arrizabalaga.

Southampton, which wore a special yellow commemorative jersey to mark 50 years since its 1976 FA Cup final win over Manchester United, joins Manchester City and Chelsea in the semi-finals.

West Ham United hosts Leeds United in the last of the quarter-finals on Monday (AEDT).

"Incredible night, the celebrations are mad. An unbelievable night for the club. We knew we could hurt them. We were a threat on the counter," Stewart said.

"We will enjoy tonight. Tomorrow we'll be back to business. It's not every day you reach an FA Cup semi-final. We have a lot of tough league fixtures between now and then."

The result heaped more misery on Arsenal, who were defeated in the Carabao Cup final by Manchester City in its most recent match, and now bows out of a competition it has won a record 14 times.

"There are no excuses for tonight," Arsenal midfielder Christian Norgaard said.

"It has nothing to do with injuries or availability. We had a really good team on the pitch that should have been competing on a high level.

"We need to pick ourselves up. We have two big competitions left to compete in."

Southampton manager Tonda Eckert extended his unbeaten run to 15 games in all competitions. Although his side had to soak up long periods of Arsenal pressure, it deserved its victory.

Southampton took the lead after a horror moment at the back for Arsenal defender Ben White.

A simple aerial cross from James Bree was missed by White and fell perfectly for Stewart to collect and fire past Kepa.

It came close to a second when Scienza’s dipping shot from the left-hand side of the box hit the top of the crossbar.

But Arsenal was level on 68 minutes as substitute Gyokeres side-footed into the net from 10 yards after a fine run from Kai Havertz teed-up the chance.

It looked the most likely to go on and win it, but with the clock running down, a quick break from Sou.thampton created the chance for Charles, who could not miss from 12 yards.

Arsenal manager Mikel Arteta could not hide his disappointment after seeing his side dumped out of competition, suggesting the team’s poor defending was the major contributing factor.

"The result and especially the way we conceded the two goals [were disappointing]," Arteta said.

"We had so much dominance in and around the box. We conceded the first goal in a very unusual way for us, the second one from direct play as well.

"We had two massive chances and needed to capitalise on that. If you make the defending errors we made today, it's very difficult to be in the semi-final."

Arsenal was without several first team regulars for a match played in driving wind and rain, but Arteta refused to blame either of those factors and was not surprised by the test Southampton handed out.

"They are a very good side on a very good run and you have to congratulate them," he said. "You have to adapt to the wind, the injuries. You have to adapt to difficult situations in the season. Now we have to show what we are made of.

"That [Arsenal] team had very good moments. They should have capitalised and be going to Wembley, and we haven't done it."

Eckert, meanwhile, is now unbeaten in 15 matches in all competitions with the Saits, but he is keeping his feet firmly on the ground.

"We put on a good shift today. It was a challenge, we knew it was going to be a tough game. The second half always has the chance to shift and we reacted quite well," he said.

"You always need to find a balance, it's not going direct for the sake of going direct. You need spells with shorter solutions and we had a good mix today.

"Belief is always there, it's not been a problem. The reality is that the game is close. It's going to be nice to celebrate today but we open up Wrexham and Championship football tomorrow."