Eduardo suffered the injury in a challenge with Birmingham's Martin Taylor last February.
"I am very happy to have him back because he gives us options," Wenger said. "He can play on the flank, he can play central, he can play behind the striker or up front on his own. It is fantastic for us. Of course, everybody is happy for him. It was good to see us play with the handbrake off. Eduardo played a big part in that. He is intelligent, talented, he understands quickly what is happening and reacts well to every situation. That is why he is a striker."
Eduardo scored the first goal in the 19th minute and the third on a penalty kick in the 60th minute. He went off eight minutes later, suffering from a slight hamstring pull, to a standing ovation.
"It was the best day of my life because it proved I can play again," he said. "It was a special moment to score and very emotional. I had tears in my eyes. I celebrated by kissing my wedding ring because my wife Andreja, daughter Lorena and family supported me right through this."
Arsenal, which also got goals from Nicklas Bendtner and Robin van Persie, hosts Burnley in their delayed fifth-round game.