The competition raised more than $5 million for coronavirus relief charities and also marked the return of live televised golf.
No spectators were allowed in to watch the match and players completed the course without caddies.
Trump, a lifelong golf fan, dialed into NBC’s coverage to say he hoped sport would be returning to normality as soon as possible.
“We want to get sports back, we miss sports, we need sports in terms of the psyche of our country,” he said.
“We really want to see it get back to normal. So when you have all those thousands, tens of thousands of people going to your majors and going to golf tournaments, we want them to have that same experience.
“We don’t want them to be having to wear masks and, you know, be doing what we’ve been doing for the last number of months.”
World number one McIlroy has previously played golf with Trump but last week said he would decline a future invitation after the way the President had tried to “politicize” the pandemic.
“It’s just not the way a leader should act and there is a bit of diplomacy that you need to show, and I just don’t think he’s shown that, especially in these times.”
Trump did not respond directly to the Northern Irishman but said he enjoyed getting to know a number of professional golfers.
“A lot of them are very political. Some like my politics very much and some don’t. The ones that don’t I don’t get to see as much,” he said.
The recent event comes ahead of another charity golf match this Sunday when Tiger Woods and Payton Manning take on Phil Mickelson and Tom Brady in what’s being dubbed, ‘The Match: Champions for Charity.’