Evans was involved in an altercation with Cisse during the first half of the game and the pair appeared to spit on each other as they argued.
A statement released by Evans on Thursday denied he had spat at Cisse and that he was unaware of any incident.
Van Gaal has echoed these sentiments and backed his player amid suggestions he could face a six-match ban.
Speaking about the incident, van Gaal said: “As I’ve said in last night’s press conference, Jonny was not aware that he was spitting.
“It’s a natural thing for a human being, it wasn’t his intention. I cannot imagine that Jonny Evans could do something like that, and he’s also said that. I believe him, so the matter is done. I think the FA is very wise.”
Evans may have denied any knowledge of the incident but TV replays showed him spitting in Cisse’s direction moments before the Newcastle striker returned the favour from only a few inches away.
Having denied the allegations, any charge brought to Evans by the FA will inevitably be appealed by the Northern Irishman.