The Manchester City striker was Bosnia's top scorer in World Cup qualifying with 10 goals but was almost anonymous against the Egyptians in the Innsbruck encounter.
"Dzeko didn't deserve so much criticism for a poor performance in a friendly, as anyone can have a bad day," Susic told reporters.
"Many players had a bad day but the fan reaction was unfair as we missed several key players through injury.
"Congratulations to Egypt because they outplayed us, especially in the second half, but we saw a lot of useful things and we will certainly be a better team in more important matches when the World Cup starts."
Dzeko also criticised the fans but was annoyed that he was forced to stay on the pitch after halftime.
"I came here with a niggling injury and Susic knew that, and he still didn't substitute me either at halftime, which was the plan, or after the break when I asked to be replaced," the striker said on his Facebook page.
"I don't know why he left me on the pitch for the full 90 minutes. I wish to thank all fans who support me but the others should be ashamed because I am a born winner and always played my heart out for the national team."
Around 10,000 Bosnian fans packed the Tivoli stadium but it was a small band of Egyptian supporters who were making the most noise after Gedo and Chelsea winger Mohamed Salah scored classy second-half goals to wrap up the victory.
World Cup debutants Bosnia are in Group F in the Brazil finals, alongside Argentina, Nigeria and Iran.
- Sports & Recreation