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.
West Ham will now meet Cardiff in one semi-final playoff, while Blackpool will play Birmingham in the other. Those games are decided over two legs with the final at Wembley on May 19.
Southampton, relegated from the Premier League in 2005 and then to the third tier of English football in 2009 after going into administration, were never going to lose their chance of a second successive promotion after taking an early 2-0 lead against relegated Coventry with goals from Billy Sharp and Jose Fonte.
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."
