The result leaves the door open to teams chasing down City's third-place in the final weeks of the season.
“The result, of course, it’s a missed opportunity today, we know that,” said Guardiola. “They defend so deep – in the first half, after 15 or 20 minutes, I realised we need the strikers especially to break them because we didn’t expect them to be so defensive.
“We couldn’t get the rhythm. The second half was better and in the last 30 minutes we had a lot of chances, but it’s always difficult against a team that plays that way.
“Today we missed the crosses, the second ball, one player in the 18-yard box to dribble and shoot.
“Second balls and set pieces - this kind of stuff we miss a little and unfortunately, we could not get the goal we needed. We could not convert."
Southampton free to play as they like
On Saints' tactics, Guardiola refused to complain, despite criticism from City defender Ruben Dias.
The manager continued: “(Southampton) can do whatever they want. For many years here we faced teams with different approaches and a team that’s been relegated to play in that way.
“It’s our duty to break them, that’s what we have to do. Many times they play five or six at the back.
“It’s difficult - you have to break it with transitions and creativity, free-kicks, reactions. We had the chances when you review it, but we couldn’t score.
“It happened. Now, prepare the final, and less time Bournemouth and then Fulham.
“We have three games left - the FA Cup and two games in the Premier League and I didn’t expect anything different from one month ago in that that we will need to fight until the end.”