City were forced to come from behind late on as Jeremy Doku and Nico Gonzalez's goals canceled out Saints' opener from Finn Azaz.
"Over big parts of the game, it was an outstanding performance from the boys. In these games, you're not going to have a lot of moments," he said.
"You know that you will always get a couple. I think we had a very big one in the first half with Leo Scienza; it's a very tight offside decision.
"And then we had a couple in the second half. If you want to or not, they're going to push you down there, so you have to defend a little bit deeper.
"We had a look at how they scored their goals this season, and there aren't too many goals from outside of the box. Unfortunately, it was two today."
Eckert added: "These games are never over, if you see and you look at the record of City over the last few years, all of their games in April and May.
"There aren't too many that they give away at this part of the season, so we knew that those 10 minutes after scoring would become very long.
"I think that we've defended very well over big, big spells, and then it speaks for itself that it's two goals from outside of the box to win the game.
"I think we've done absolutely everything to represent this football club in the best way possible. We wanted to give the supporters a final here.
"We were very close, so it's quite natural that there's a good sense of disappointment straight after the game, but we have a big week coming up.
"There's going to be a test of maturity for us to put this game together as quickly as possible because we need another top performance on Tuesday."