The pair tussled during the first half of the Premier League game at St James' Park which the Manchester side won 1-0 and Evans appeared to spit towards Cisse as he lay on the ground before the Newcastle player got to his feet and returned the compliment.
"I didn't see it. I don't think Jonny Evans is a spitter," Van Gaal told the BT Sport. "Maybe spitting on the floor but we are on the bench and you cannot see from there."
Newcastle manager John Carver was also unaware of the incident.
"I haven't seen it," he said.
Newcastle were unfortunate not to get an early penalty when Chris Smalling brought down Emmanuel Riviere and as the game looked to be heading for a goalless draw until Newcastle keeper Tim Krul booted a clearance straight to Ashley Young who scored in the 89th minute.
"I think we have dominated for 90 minutes, maybe our best match of the season, especially in an away match we deserved the victory," Van Gaal, whose side are coming under pressure in the battle for a top-four slot, said.
"We didn't reward ourselves in the first half. It was a narrow escape because our rivals have won also so it's a rat race.
"We have created a lot of chances and could have scored much earlier. They also made two big chances and I think David de Gea rescued us at that time."
United stayed fourth in the table and remained on course for a Champions league place despite another unconvincing performance and they were indebted to Wayne Rooney's persistence for pressurising Krul into the mistake which led their goal.
"It was a crazy run from Wayne Rooney, a lost ball, that shows the fighting spirit in this team," Van Gaal said.
"We want to win. All my changes were to win, not to hold the result."
(Reporting by Ed Osmond)
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