Boro's decent run of form came to a juddering halt and Mowbray admitted they had failed to cope with the loss of a number of key players as they were out-fought and out-thought by Nigel Clough's improving side.
"It's disappointing to lose any game but you have to give them credit," Mowbray said.
"They are a team full of energy and some very good players. We never got to the races at any stage of the game today.
"We've done okay so far this season but for whatever reason, we didn't get going at all today. But we will get stronger as the season goes on and players are back from injury.
"There was probably almost a team missing today but I don't want to use that as an excuse. Derby played well today and good luck to them."