On his 25th Premier League appearance Che Adams scored his first and the only goal of the game to ensure Ralph Hasenhuttl's side came away with all three points.
Story of the match
It was a lively start to the match with both sides looking to start strong and inflict damage upon each other.
Southampton looked aggressive, determined and had the look of a team fighting for something despite being well clear of relegation and are probably too far away to reach a European place with only five games to go.
In despite of that the Saints were determined to get something from the game and were duly rewarded for their positive start with the opening goal in the 17th minute.
City typically started their attack by playing out from the back but were caught out after Oleksandr Zinchenko was disposed easily by Saints midfielder Stuart Armstrong.
The Scotsman laid the pass a few yards forward to Adams who noticed Ederson way off his line, and amazingly had the vision and technical ability to lob the Brazilian from 40 yards out to give the south coast side the opening goal of the game.
Adams, in his debut season following his signing from Birmingham City last summer had not scored all season in the league but produced a shot of superlatives to ensure his first goal in England's top division would be a memorable one.
Southampton were full credit for the opener having hustled and harried Manchester City as well as giving them very little time on the ball, something we all know Pep Guardiola's sides love to control.
Eventually City moved up a gear and started asking more questions of the Saints defence with Joao Cancelo picking out Gabriel Jesus from the right, however the striker could only divert the Portuguese man's cross over the bar.
The Blues were coming in droves at Southampton's back four with David Silva's low ball from the left being cleared by Jan Bednarek over his own goal.
It was only the beginning of the onslaught for Southampton who had to call Alex McCarthy for the first time in the match. Jesus' outside of the boot pass went to the left to Raheem Sterling whose fierce left footed strike forced a good save from the keeper.
The action kept coming thick and fast with Kyle Walker-Peters failing to clear the second ball properly thus falling to Fernandinho who struck the post left of the goal from twenty yards out. Just as Southampton thought they were in the clear, the ball broke right to Bernardo Silva who produced a fine cross to one of the most unlikeliest on the pitch to win a header, David Silva however he rose high to meet the cross and force another excellent save from the Englishman in goal.
After a few minutes of rest-bite for the Saints, City were back again, Cancelo driving from right-back to midfield fed the ball right to Riyad Mahrez who typically shifted the ball from his right to his left foot and produced another fine save from McCarthy.
Since the opener, Southampton were completely penned back in their own half but had a good chance to double their lead before half-time. 40 yards from goal, Walker-Peters sent a ball over the top catching out the entire city defence, however fortunately for them, the usually clinical Danny Ings could not connect the on-loan full-back's cross and sent his shot over the bar whilst stretching.
Guardiola would have been pleased with what he saw during the first half and would have urged his side to keep doing what they were doing as the goal would surely be on its way.
Early in the second half Pep's prediction nearly came true following a flick on by Jesus following a Mahrez corner, however no one could get the telling touch allowing Southampton to survive again.
There are always one or two games in a season where the keeper would play the game of their lives and unfortunately for City, today would be that day. Moments later, McCarthy produced a fine reflex save to deny Jesus' header following Laporte's superb turn and shot which was initially blocked by Walker-Peters.
City were relentless as they threw the proverbial 'kitchen sink' at the Southampton defence, but credit to the Saints who stood tall and kept on putting their bodies on the line, Bednarek and man-of-the-match Jack Stephens in particular.
In despite of City's dominance, Southampton almost caught the Blues on the counter attack following a driving run from the left by substitute Shane Long who fed Armstrong, thankfully for City his effort was straight at Ederson.
As in every game with the score on a knife-edge, there would always be one great chance for the losing side, and in City's case, two excellent chances. The first falling to Bernardo Silva who could not react quick enough after the near faultless Alex McCarthy failing to get any contact on Cancelo's cross with the ball eventually squirming away for a corner.
The last kick of the game, a free-kick 20 yards out with Kevin De Bruyne standing over it, thankfully for the Saints players,staff and the thousands of fans at home the Belgian's effort went into the wall with the effort summing up an ultimately frustrating day for Pep Guardiola's men who succumbed to their ninth league defeat of the season.
Takeaways from the match
The saints go marching on
It would have been an easy decision to sack Ralph Hasenhuttl following their nine-nil drubbing by Leicester City last October but immense credit should be given to the former RB Leipzig manager who has turned the ship around magnificently since then.
Southampton after several years of instability following Mauricio Pochettino departure in 2014 have finally found a man who can deliver the football that the Argentine gave Saints fans and can look forward to a potential top half finish and even more exciting 2020/21 Premier League season.
Defensive frailties a concern for Pep
The league season is all but over for Pep's side as they failed to retain the title for a third season and are likely to finish second. However there is still plenty to play for in the FA Cup and the UEFA Champions League but should City continue to defend the way they have been they can forget about retaining the cup as well as seeking glory for the first time in Europe's premier competition.
With a second leg still yet to be played against in form and LA Liga champions elect Real Madrid coupled with an FA Cup semi-final against Arsenal, Pep will know that a great deal of defensive work needs to go in should City want to be successful in their two remaining competitions.
Up next for both
Tough opposition keep coming for the Saints as they travel to Merseyside to take on Carlo Ancelotti's Everton at Goodison Park on Thursday evening.