Having finished third in the inaugural finals, Sunday's 2-0 defeat to the world's top-ranked side in Leuven means they cannot make the second edition next year.
Youri Tielemans' deflected strike and a fine Dries Mertens free-kick saw Belgium run out 2-0 winners at Den Dreef, where Roberto Martinez's men had to dig deep as England applied constant pressure in the second half.
But the visitors lacked the required cutting edge to secure a victory from a game that Southgate felt his side performed better in than last month's 2-1 win against the same opposition at Wembley.
"We're always disappointed to lose and to lose tonight puts us out of this competition," the England manager said.
"But I've got to balance that because I have to focus on performances. If you get performances right, then you will normally win matches.
"Some days that won't happen for you. I think today we were better than we were at Wembley.
"We created more opportunities, we had more of the ball.
"I think two moments in the game - a deflection for the first goal and the second goal I don't think is a free-kick - were the turning points.
"After that they had a couple of counter attacks - that is inevitable when you're pushing and pushing as we were.
"But I'm so impressed with the performance of the players.
"We've learned a lot about a lot of players - not only their ability but their mentality.
"There were several players in the very early stages in their international careers who were excellent.
"Jack is the obvious one. His performance was outstanding.
"But I also thought Bukayo (Saka) as well coming into a game like that as a very young player against an experienced player like (Thomas) Meunier had an excellent game on the left when he came into it.
"Tyrone (Mings) as well. That's a level up from the games he's been in with us before.
"But also some other experienced players who played very well, so I take a lot of positives from it, although of course we don't want to lose football matches."
Sunday's defeat means that qualification from Group A2 is beyond England heading into Wednesday's Wembley encounter with relegated Iceland.
Grealish may well be rested for that match having starred from the outset against the Republic of Ireland and Belgium, but the Aston Villa playmaker must have surely sealed his spot at next summer's European Championship.
"I think, firstly as a person, since he's come into the camp he's impressed us with his approach," Southgate said.
"He's been curious to find out what we're looking for from him. He's taken that on board with these performances and in training.
"He transferred his club performances into international football tonight against a top-level opponent, so we couldn't have been happier with what he did.
"He should be really proud of his performance and, yeah, as I say, I think he really stood up against as tough an opposition as you're going to face."
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