Fulham looked to be on their way to a first win in seven Premier League games after Ashkan Dejagah gave the London club a 1-0 lead at fellow strugglers West Brom.
Stekelenburg pulled off a number of fine saves to preserve the visitors' advantage but turned from hero to villain four minutes from time as he allowed substitute Matej Vydra's tame effort to sneak under his body and over the line.
The Dutchman's error prevented Fulham from moving off the bottom of the table, but Magath was quick to defend the former Roma keeper.
"He was (playing) very well and it was a shot from only a few metres," Magath said.
"Such things can happen, I don't see the keeper in this situation as making a fault. I don't blame him."
Fulham are four points adrift of safety at the foot of the table but, although Magath accepted his side made too many mistakes in the second half, he remains confident that they will avoid relegation.
"The players are disappointed because we are so close to the first three points," he added.
"It was a typical game from two teams that play against relegation, there was a lot of fight and that is what I want my team to do.
"Although I was very satisfied, especially with the first half, in the second I think we have made too much mistakes.
"I am satisfied with our game today, I would prefer to win but I think have done it quite good and we have to work step by step and for the first days I am satisfied.
"I was sure before the game (that Fulham will stay up) and I am sure after the game. We were close to a win and the next game we will win. It is only against Chelsea."
