West Ham United, who could have pipped Southampton if results had gone their way, finished third after beating Hull City 2-1 at Upton Park and will take part in the play-offs along with Birmingham City, Blackpool and Cardiff City.
Champions Reading, who clinched the title last week, lost 2-0 at Birmingham but finished top with 89 points from their 46 games. Southampton, who took the remaining automatic promotion spot, ended with 88 points and West Ham 86.
Further strikes from Jos Hooiveld and Adam Lallana made sure of three points and Saints manager Nigel Adkins told the BBC: "A lot of people have put a lot of hard work in here - the players deserve all the plaudits they'll get as everyone at this club has worked their socks off since I've been here.
"Southampton are back in the Premier League, and I'm a happy man - I'm proud and honoured."
The mood at Upton Park was subdued as news of Saints' early goals filtered through to the crowd, although West Ham did duly win with two goals from former England striker Carlton Cole.
Manager Sam Allardyce identified his team's shortcomings as they failed to clinch automatic promotion back to the Premier League after relegation last season.
"We dropped too many points with draws at home," he told Sky Sports. "But we were a bit unlucky as in the last four or five seasons 86 points was enough to win automatic promotion."
