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Raphael Guerreirohad his second-half goal ruled out by VAR after Haaland's blocked shot appeared to loop up off the top of his arm before he volleyed home.
Dusseldorf twice hit the post before substitute Haaland headed home in the 95th minute to secure a 1-0 victory and ensure the Bundesliga title race remained alive, withhead coach Lucien Favre injuringhimself celebrating the dramatic goal.
While the handball decision did not cost them on this occasion, they missed out on a potential penalty in a 1-0 defeat to leaders Bayern Munich last monthwhen a shot fromNorway international Haaland was deflected wide off the arm of Jerome Boateng.
In the following game against Paderborn, Dortmund conceded a penalty when Emre Can was adjudged to have handled the ball when sliding to block a shot from Mohamed Drager.
Asked about the decision to disallow Guerreiro's goal, Haaland said: "I haven't seen the replay yet, but I have the feeling this handball rule is currently only against us."
Haaland sat out Dortmund's previous two games due to a knee problem and, after replacing Axel Witsel in the 61st minute, was pleased to be back among the goals.
"The team needed something up front and I was just waiting for my chance and luckily I got it in the end, and it was a goal, so it was very nice," he said.
"We had some chances and they also had chances, so I don't want to say we were lucky but three points is very nice.
"Dusseldorf had good tactics and made it difficult for us, but good teams win even on bad days."
After the game, Dortmund received a welcome boost with the news that goalkeeper Roman Burki is set to sign a new contract with the club, following reports linking him with Chelsea .
"I'm delighted and hope we can get together in the next week to get everything sewn up," Burki said, quoted by newspaper Ruhr Nachrichten .
"I feel very comfortable here, I've been through a lot with BVB over the years and always felt the love of the club."