Hart described referee Wolfgang Stark's decision to dismiss Rooney as "the most pathetic sending-off I've seen in my life."
The Manchester United star will miss the start of next summer's finals through suspension after his challenge on Miodrag Dzudovoic.
Hart said: "I saw it all. It was pretty pathetic. It was supposedly a kick but it was pathetic.
"It was the most pathetic sending-off I've seen in my life.
"I feel for Wayne, who is disappointed, because 10 minutes later I saw Danny Welbeck take it on the jaw and nearly have his head knocked off.
"I was thinking 'what's happened there?' and 'why is that not a red card?'
"That's football and that's what we have to deal with these days. There was nothing we could have done at the time.
"We moved on as a team, Welbeck did really well upfront after he came on and did a great job."
He said: "We are over the moon. It was a case of 'job done.' We have got England as a nation to a major tournament next summer.
"We are a good bunch of players, a proud bunch of players. We played for our country, knowing we had to get to get to a tournament and we've done that.
"It was a difficult atmosphere and they are a good side but we are there although we wanted the win and the manager said we got sloppy in the last five minutes.
"We showed true grit and true determination and I am so proud to be part of this England team."
England led 2-0 through goals from Ashley Young and Darren Bent's fourth in his last five internationals.
But Elsad Zverotic reduced the arrears on the strike of half-time and Andrija Delibasic's late header rescued a point for the home side who have qualified for the play-offs.