Palace winger Wilfried Zaha was a menace throughout as the hosts moved up to fourth, leaving Boro in sixth and five points from an automatic promotion spot.
"If we are looking for reasons, the amount we put in against Leeds in such a physical game (1-0 win on Tuesday) appears to have taken it out of some," Mowbray said.
"That appears to be the case. But there are no excuses. Individual errors cost us for the goals. We knew they had talented forward players going forward. But my players are sitting there disappointed.
"We lost four goals at Ipswich a few weeks ago. We can't keep doing that.
"We are still in the top six and our ambitions are to remain there. We are capable of winning matches. We have to get back to our old form, but at the moment that seems a long way away.
"Three of our back four are out at the moment, but we have to get on with it. Justin Hoyte, Jonathan Woodgate and Seb Hines are injured and we have to take it on the chin."