Ryan Gauld celebrated his first call up to the Scotland Under-21 set-up earlier this week with goals either side of half-time with John Rankin and Andy Robertson also on target for the visitors.
Motherwell were without three of their first-choice defenders for the game but McCall refused to make excuses for his side's defeat and showered Jackie McNamara's side with praise.
"You don't want to lose at home by that margin but in all my time here that was the best performance of any visiting team and I include Celtic, Rangers and European opponents in that," McCall said.
"Sometimes you have to hold your hands up and say you were well beaten. I said at the start of the season that they had a good, young squad and they came here on the back of a couple of impressive away displays.
"We just have to lick our wounds and take it on the chin."
United manager McNamara was delighted with the performance from his players and insisted his side have now put in two good displays consecutively following their draw away at Celtic last week.
"Motherwell were on a great run at home and we knew it would be difficult," he said. "But I thought a lot of our boys showed great energy from start to finish, and Andy Robertson was terrific and got his reward with his goal in the final minute.
"It would be disrespectful of me to say that Motherwell were under-strength at the back but it was really nice of Stuart McCall to say it was the best away performance he has seen at Fir Park.
"I thought we played very well against Celtic last week without taking our chances.
"Today I thought we created as many chances and the only worry I had was that we only had a two goal lead at half-time."
McNamara also explained why he withdrew Gauld from the action with a quarter of the game remaining.
"I was reluctant to take him off but he took a bit of a dunt before his first and was a bit groggy at half-time so we took him off before the end for his own sake," McNamara said.
"Hopefully he will be okay for the Scotland Under-21s."