The 49-year-old was appointed as Ralph Hasenhuttl's successor on November 10, penning a three-and-a-half-year contract until the summer of 2026.
However, Jones has failed to turn the club's fortunes around and has endured a difficult spell at St Mary's, losing nine of his 14 games in charge across all competitions.
Eight of those defeats have come in nine Premier League fixtures, including Saturday's 2-1 home defeat against 10-man Wolverhampton Wanderers - a game which the Saints were leading heading into the final 20 minutes.
Jones's only Premier League win as Southampton boss was a 2-1 success away at Everton on January 14, while he claimed two victories in both the FA Cup and EFL Cup, including an impressive 2-0 quarter-final triumph over Manchester City in the latter competition.
The former Luton Town coach was backed in the January transfer window as Southampton spent close to £60m on five new signings, including the club-record addition of winger Kamaldeen Sulemana on deadline day.
However, the league defeat against Wolves has proved to be the final nail in the coffin for Jones - who lost the support of the St Mary's faithful - and the Welshman leaves Southampton rooted to the foot of the Premier League table, four points adrift from safety.
A brief statement on the club's official website has also confirms that first-team coaches Chris Cohen and Alan Sheehan have left the club.
First team lead coach Ruben Selles has been placed in temporary charge while Southampton search for a successor.
Speaking after the defeat against Wolves, Jones said: "It's very tough, not just myself, for the guys, for the club. I thought for 60 minutes we were really good - first half we were excellent, probably as good as we've played at home.
"We were front-footed, aggressive, went after the game, created enough chances to have taken more of a lead, but we didn't.
"In the second half we had a real glorious chance to go two up, and you just fear then. We tried to make positive changes to make sure we stayed front footed, but it wasn't to be.
"They showed a little bit more quality in the final third than we did. They scrambled in one goal, but the second goal is a good finish and we just needed to show a little bit of that.
"It's understandable. With the team, what they do and everything it's really understandable that confidence is low and they're a bit worried, but I didn't really see any issues."
Southampton, who have won only four of their 22 Premier League games this season, will travel to Stamford Bridge to face Chelsea in their next match on Saturday.
More to follow.