Pep Guardiola’s dethroned champions were expected to waltz to three points on England’s south coast and pull level with second-placed Arsenal on 67 points.
But although the FA Cup finalists dominated possession and had 26 shots, they could not break their opponents down, despite the return of top-scorer Erling Haaland.
Third-placed City, who play Crystal Palace in next week’s FA Cup final, remain well-placed to finish in the top five, which would secure qualification for the Champions League next season.
But Villa, in sixth spot, are now just two points behind them, on 63 points after their 1-0 win at Bournemouth.
“(Southampton were) playing to defend and defend and defend and waste time,” Guardiola said afterwards. “We take that point still, it’s in our hands.
“Didn’t expect them to defend so deep. Defensively we were so good but unfortunately we missed the last actions.”
There was an explosion of joy among the home fans at the final whistle, even though Southampton’s relegation fate was sealed weeks ago.
The point for managerless Saints takes them to 12 for the season, meaning they have avoided the tag of being the joint-worst team in Premier League history.
They are now one point clear of Derby’s tally of 11 in the 2007/08 campaign.
“Everyone knows it’s been a difficult season for us,” said Southampton goalkeeper Aaron Ramsdale.
“That one was for the fans and also the lads who have given everything. A lot of Mondays coming in after heavy defeats. Today is a relief.”
Ollie Watkins’ goal in the dying seconds of the first half gave Villa a narrow win at Bournemouth.
In scoring, England forward Watkins became the club’s all-time top goalscorer in the Premier League, his 75th goal taking him past Gabriel Agbonlahor’s tally of 74.
Villa’s Jacob Ramsey was dismissed after a second yellow card with about 10 minutes to go, adding a touch of jeopardy.
Antoine Semenyo flashed a shot just wide and Emiliano Martinez saved smartly from Evanilson, but the 10-man away side held on to secure a crucial three points.
Unai Emery’s team, who suffered the crushing disappointment of defeats in the Champions League quarter-finals and FA Cup semi-finals in recent weeks, can still finish the season on a high.
Elsewhere, Brentford and Brighton both won to keep alive their European ambitions.
Brentford beat already relegated Ipswich 1-0 for their fourth straight win, climbing to eighth in the table, which may be enough for European football next season.
Kevin Schade headed home from Bryan Mbeumo’s corner in the 18th minute for his 11th Premier League goal of the season.
“I see a strong team on form, we have got the momentum, which is important,” said Brentford boss Thomas Frank.
“We are close to finishing eighth, which would be the best position ever in the league. We are laser-focused on what we can do.”
Brighton beat Wolves 2-0 at Molineux and are behind Brentford only on goal difference.
Danny Welbeck scored a first-half penalty and Brajan Gruda added a second in the 85th minute to secure the three points.
Everton beat mid-table Fulham 3-1 courtesy of goals from Vitaliy Mykolenko, Michael Keane and Beto.
Fourth-placed Newcastle host Chelsea, a place below them, on Sunday, with seventh-placed Forest in action against relegated Leicester.
Champions Liverpool play Arsenal, who are not yet certain of finishing in the top five despite being the closest challengers to Arne Slot’s men this season. (AFP)
