The Manchester United manager responded to three successive goalless draws by starting with Martial as his central striker and playing the England captain in a withdrawn role in the Champions League Group B clash.
But with the score locked at 0-0 he hauled the Frenchman off and pushed Rooney up front, a decision that was loudly derided by what seemed a hefty majority inside the stadium.
Rooney, though, paid his boss back by heading home the only goal of the match in the 79th minute, Michael Carrick and Jesse Lingard having combined to present the opportunity.
Van Gaal was well aware his decision was not welcomed in the stands, but was content with the outcome.
Asked if he had heard the crowd's reaction, the Dutchman said: "Of course, I am not deaf.
"That is the opinion of the fans. Afterwards they shall not be disappointed by the decision of the manager.
"I'm very happy because I put him again in the striker's position and he scored."
Van Gaal was otherwise keen to spread the praise on a night when the Red Devils moved a point ahead of PSV Eindhoven at the top of the group.
"I back all my players, not only Wayne Rooney. Wayne Rooney is always centre of attention, I have to answer always about Wayne Rooney and now again.
"Wayne is Wayne, he shall always contribute in a game.
"It was a fantastic goal. The tackle of Marcos Rojo was fantastic, the pass of Michael Carrick and the cutback of Jesse Lingard. Then the header of Rooney.
"It was fantastic. I'm very happy about the performance of my players, also about the result and also the fact we are top of the group."
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