Union took the lead midway through the half when Oliver Burke curled home a superb finish in the 57th minute, his first goal in nine games, before Leipzig hit back almost immediately through Tidiam Gomis, who had come off the bench to equalise in the 60th minute. Ilyas Ansah restored the hosts' advantage with a header in the 63rd minute, and Tim Skarke sealed the victory in the third minute of stoppage time.
Leipzig's defeat extended their winless run away from home to three matches and left them unable to reduce the gap on Bundesliga leaders Bayern Munich, with third-placed Borussia Dortmund able to overtake them if they win on Sunday.
Werner said the match unfolded as he had expected, but key moments swung the contest. "We expected this sort of game," Werner said. "In my view, we dealt with the challenge well in the first half. But in the key moments, Union were physically stronger in the tackles and stuck together."
Reflecting on the pivotal passage that saw Leipzig take the lead only to concede twice within minutes, Werner added: "We had a great opportunity on the counter before their second goal. And Union found the back of the net directly after that. That might have been the decisive moment. After that, we lost our heads a bit."
Werner also highlighted the relative youth of his squad. "We're a young side, and experience plays a role when you concede goals. We'll learn from it, and we've been learning pretty quickly all season. Today, the more experienced team won."
Leipzig will return home to host Bayer Leverkusen in their final match before the winter break. Werner insisted the focus has already shifted to that game. "We're disappointed today. But we have a home game against Leverkusen next week. That's what we're going to focus on now," he said.