Paco Alcácer grabbed the opening goal of the game inside the opening three minutes but Harry Wilson's smart finish levelled the scoreline heading into half time.
Thomas Delaney and Jacob Bruun Larsen gave Borussia Dortmund a two-goal cushion after the break, although Rhian Brewster halved the deficit with a stunning penalty later in the second half.
Lucien Favre's Dortmund held on for the win at the
"How we conceded goals was a lack of organisation, but it is very difficult to have that at this stage.
"I don't like what I see in a game in pre-season very often but there is always a reason for it. I am not over the moon with our performance but I know there is lots to come."
The Reds still have four more pre-season games to get through before their curtain-raiser against Premier League champions Manchester City in the Community Shield.