Yan Valery's wonder strike sent the Saints in ahead at half-time, before a second half fight-back from the home side overpowered the visitors' plucky efforts, despite a largely positive performance from Southampton.
After watching De Bruyne limp off in first-half stoppage time, Guardiola then saw Stones leave the field minutes after the restart on his return after three games out with a groin problem.
As Romelu Lukaku sprinted away to celebrate his 88th-minute winning goal, surely any lingering doubt over the identity of the Manchester United manager for the 2019-20 season was carried away with him.
Six minutes later, Pereira released Lukaku with fine footwork and the striker side-stepped a defender before drilling a low shot with his weaker right foot into the bottom corner of the net.
Dalot leathered a long-range strike just wide and scooped over as United looked to press home their advantage, but Saints got a set-piece opportunity after Young was adjudged to have fouled Stuart Armstrong.
City moved two points clear of Liverpool, who play Everton in a local derby today.
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NASA is providing eight billion USA dollars for SpaceX and Boeing to build and operate these new systems. Saturday's flight "is the next critical step in putting people on Dragon", he said.
The former Everton man has been dropped and shunted out wide in recent weeks following a hard start to this season but it is testament to his resilience that he is back in the team and back in fine form in front of goal.
There was still time for more drama, though, as Southampton midfielder James Ward-Prowse curled home a stunning free-kick.
"So this has been a strategy of United's which I presume is about keeping the wage bill down, so the calculation was: 'we're paying De Gea this much money, if we give him an improved contract now, that's gonna cost us X million more over the next two years that we don't have to spend". My team did fantastic and the boys did great in the second half.
"The belief is there, they have gone so long without losing games (domestically) and are raring to go".
"They were class finishes from Romelu Lukaku and I am so pleased for Andreas Pereira".
This was a Premier League record ninth time that United had come from behind to beat Saints and former striker Solskjaer certainly felt like this was a throwback to the Sir Alex Ferguson era. "It's like every manager doesn't like to lose and we had a big chance but it was not enough".