Evans appeared to spit in the direction of striker Papiss Cisse in the opening period, with the Senegalese seemingly returning fire immediately.
Van Gaal claimed not to have seen the altercation, although he insisted the Northern Irishman would not intentionally do such a thing.
"I didn't see that from the bench," he told reporters. "I think it was too far to see that. I cannot imagine Jonny Evans doing that."
Van Gaal's opposite number John Carver was similarly cautious when asked, saying: "I am aware of it now having seen the TV guys talking about it. I have not seen the incident, genuinely.
"I just saw a fracas on the halfway line and I need to have a look at it. The players have not mentioned it."
The controversy overshadowed another battling win from United, who took the spoils thanks to Ashley Young's 89th-minute winner.
The late goal delighted Van Gaal, with the Dutchman claiming his men got their just rewards.
"I have said in the dressing room that I was very pleased with the performance," he said after seeing United maintain their spot in the top four.
"This is a difficult ground to win. We dominated the game, but we don't reward ourselves. When you don't do that, you can end up with a negative result.
"It could have been because David de Gea made two fantastic saves. But, I have to say, Tim Krul did also.
"We have waited a long time for the winning goal but it shows the fighting spirit of our team again.
"I have said that a lot. For me, it was very important to win. All our competitors in our rat race [for the top four] have won too."