The Reds suffered their second continental loss of the season to Alexander Blessin's side, but the result was rendered meaningless for Liverpool, who were already confirmed to have won the group.
As a result, Klopp left a handful of senior players behind and called upon a selection of fringe and academy players for their final game in Group E, as Kaide Gordon, Conor Bradley, Ben Doak and Luke Chambers all made the first XI.
With an inexperienced team on the field, Liverpool were unsurprisingly second best throughout the evening and conceded to Mohamed Amoura in the 32nd minute, as the Union SG attacker got in behind the Reds' high line.
Amoura's strike was cleared following a brief VAR check, although there was still a hint of offside, sparking painful memories of Luis Diaz's wrongfully disallowed goal against Tottenham Hotspur in September.
The Reds did draw themselves level through a fierce Jarell Quansah strike just seven minutes later, but Cameron Puertas then caught Caoimhin Kelleher out at his near post to ensure a third-placed finish and spot in the Europa League for Union SG.
Speaking in his post-game press conference, Klopp conceded that Union SG deserved the three points and brushed off the questionable offside call in their inconsequential loss, saying: "I think we definitely all saw the same game, so for us it was a deserved win for Union.
"Even though I heard now the first goal might have been offside but nobody can tell properly. We will see that, but who cares? They are well set up, they are top of the table, they played a stronger side, I mixed up the team completely, so I think the changes we made, the amount of changes, were too much for rhythm.
"It was pretty intense on a really difficult pitch. It was not great and you saw how intense it was, a couple of players had cramps for Union. So, in the end we could have scored the equaliser and it would have been nice, we would have loved to have got the point here. For some it was a really important experience and for others good for rhythm.
"I saw good performances and, of course, as a team it is not a fair assessment if I say now they are top of the table in Belgium and we come here, bring kids - altogether that's really difficult. But I thought we gave it a go and that's OK for me. Nobody got hurt, nobody is injured, so we recover, go home and go again."
Despite falling short in Belgium, Liverpool's loss was still a momentous occasion for Quansah, who expertly controlled a Curtis Jones's corner before firing in his first Reds goal, a few weeks on from having a late leveller against Toulouse ruled out.
Reflecting on the 20-year-old's opening goal for the Merseyside giants, Klopp added: "It was important. I think we all know against Crystal Palace that he played not a bad game against Palace but if you are then that involved in kind of the penalty, a strange one, but we are involved, that's not cool.
"And I am really happy that he could see the other side of the metal and score this goal today. That's what I liked the most from all of the boys - that they really gave it a proper go."
By finishing top of Group E, Liverpool have avoided a playoff double-header with an eliminated Champions League team and will go straight into the last 16, the draw for which will be held in February.
The Reds now return to Premier League duty against Manchester United on Sunday sitting one point clear of Arsenal at the top of the table, while Aston Villa are only two points worse off than Klopp's side.