For a moment, Finn Azaz's goal looked as though it would win them the game and set up a first FA Cup final since 2003.
In the end, Man City's quality, mixed with a bit of luck, proved too much for a Saints side who have again shown they can hang with the big boys.
Here's how we rated every Saints player's performance at Wembley...
Saints v Manchester City FA Cup semi final match at Wembley. (Image: Stuart Martin)
Daniel Peretz - 7.
Bailed Saints out on a couple of occasions, including an early save to deny Omar Marmoush, and could do nothing about Nico's rocket, which won the game. Fortunate not to concede after Doku beat him in a race on the halfway line.
James Bree - 7.
Was defensively solid and unlucky that Doku's effort from the edge of the box deflected off his leg and beat Peretz. Won the bulk of his duels but perhaps lacked a bit of final third quality, as none of his crosses found their target.
Nathan Wood - 8.
Continued his fine form in the FA Cup by making several vital defensive interventions, including a double block in the second half. The best performance at the back.
Taylor Harwood-Bellis - 8.
Much like Wood, he was very good at the back and dealt with City’s central threats. Remained level-headed on the big occasions during long periods under pressure.
Finn Azaz and Taylor Harwood-Bellis after their defeat to Man City.Finn Azaz and Taylor Harwood-Bellis after their defeat to Man City. (Image: Stuart Martin)
Welington - 8.
Very impressive in his first start since February, but he had to come off with an injury in the second half. Made a perfectly timed slide tackle on Rayan Cherki in the first half. Just kept winning the ball back until his body gave out.
Cam Bragg - 8.
Have run out of things to say about the academy graduate at this stage. A brilliantly timed tackle to stop a City counter best summed up his performance and development. Supped to applause after an hour.
Caspar Jander - 9.
The best player on the pitch across both teams. Was a ball-winning monster, recovering possession seven times and winning eight ground duels, including one to help set up Azaz's opening goal.
Southampton's Caspar Jander was outstanding against Manchester City.Southampton's Caspar Jander was outstanding against Manchester City. (Image: Stuart Martin)
Tom Fellows - 7.
Did a lot of hard graft up and down the right wing, as he had to drop deep to defend. Had a breakaway half-chance just after the restart, but Nathan Ake kept pace to stop him. Won two free-kicks, both in good areas.
Finn Azaz - 8.
Scored the goal that had Saints dreaming, albeit briefly, that they could pull off another FA Cup shock. Also created two chances for his teammates on an afternoon when defensive duties ranked above creative output.
Leo Scienza - 7.
Thought he had scored Southampton's opening goal in the first half when he slotted past James Trafford, only for the offside flag to deny them. Saints couldn't get him into the game on the transition often enough.
Leo Scienza looks dejected after Southampton's defeat to Man City.Leo Scienza looks dejected after Southampton's defeat to Man City. (Image: Stuart Martin)
Ross Stewart - 7.
Had to drop really deep to help his teammates defend, which massively limited what he could do in the final third. Yet, without his hard work, Saints may not have stayed in the game for as long as they did.
Substitutes
Shea Charles - 7.
Came on to replace Bragg and settled into the midfield straight away, which is easier said than done on the big occasion. Would have wanted to get on the ball a bit more, but you have to accept that City dominate possession.
Cyle Larin - 6.
He was just as limited up front as Stewart, and maybe the lack of touches is why he elected to pass backwards in the back rather than shoot in the first instance.
Kuryu Matsuki - 8.
The best performer of Southampton's subs, especially as he came on to replace Welington. Got the assist for Azaz, forced a good save out of Trafford with an edge-of-the-box effort, and raced back to block a certain City goal on the line.
Saints look dejected after their late FA Cup semi-final defeat to Man City.Saints look dejected after their late FA Cup semi-final defeat to Man City. (Image: Stuart Martin)
Cam Archer - N/A.
No rating as he came on to replace Bree after City's second as Eckert threw everything he could at Pep Guardiola's charges.
Sam Edozie - N/A.
No rating here either, as he replaced Fellows at the same time. Got on the ball twice but was unable to stop Doku beating Peretz on the halfway line, although he nearly got wiped out by his own goalkeeper.