The Three Lions went down to their first qualification defeat in a decade and their coach gave an honest assessment of their display
England topped Group A ahead of the clash at Eden Arena having taken a maximum 12 points from four games and victory would have secured their place at the finals.
Southgate felt his side were poor at the back, while a lack of quality on the ball was also highlighted as a factor in the loss.
“We’ve had a lot of credit in the last two years but we didn’t do enough to win,” he told ITV Sport .
“The performance was not good enough, simple as that.
“We probably should have got a draw but the goal we conceded was typical of chances we conceded
“I think there were things we can look back on, collectively we have to accept there were not enough good performances.”
The Three Lions made a positive start when captain Harry Kane converted an early penalty, but the lead lasted less than five minutes as Jakub Brabec punished sloppy defending to score from a corner.
Jaroslav Silhavy’s side moved level on points with England when Zdenek Ondrasek came off the bench to fire home the winner on his international debut.
England had scored at least four times each of their previous matches in the campaign to date but fell to a first qualifying loss since 2009, ending a run of 43-game run without defeat.
Southgate said his team, who had won 14 consecutive European Championship qualification games before Friday, had struggled to adjust to a tactical tweak.
They made a switch at half time but were still sloppy in the second period, according to their coach.
“We tried to change shape in the first half and it didn’t work as well as we hoped, so we changed it and we started better in the second half and had good chances to win the game,” he added, soon after the final whistle.
“But we conceded too many poor chances and conceded possession too often.
“We knew we’d have to be at full tilt to deal with the Czech Republic, but we should have been strong enough to deal with them.”
Nations League semi-finalists England resume their qualifying campaign away to Bulgaria on Monday.