Defeat means Newcastle face a fight to progress from Group F although they are still well-placed with four points from three games, the same as Dortmund.
But of even more concern to Howe were injuries to forwards Alexander Isak and Jacob Murphy.
"Isak going off was a blow and Jacob came off with what looks like a serious injury," Howe said.
Jacob looks serious, potentially a dislocation of his shoulder."
Newcastle face Wolverhampton Wanderers away in the Premier League on Saturday.
Persons:
Park, Newcastle United's Alexander Isak, Lee Smith, Newcastle United's, Eddie Howe's, Howe, Alexander Isak, Jacob Murphy, Sweden's Isak, Callum Wilson, Murphy, Isak, Jacob, We've, That's, Elliot Anderson, He's, Martyn Herman, Hugh Lawson
Organizations:
Soccer Football, Newcastle United, Borussia Dortmund, James, Newcastle, Champions League, Wolverhampton Wanderers, Premier League, Thomson
Locations:
Newcastle, Britain, NEWCASTLE, England, Dortmund