The midfielder's first goal for United turned out to be a special one, as he collected a loose ball about 25 meters out and sent a dipping shot into the corner.
"I have to admit we got a bit lucky", Mourinho said.
Crystal Palace: Wayne Hennessey (out of 10) 6, Aaron Wan-Bissaka 6, Martin Kelly 6, James Tomkins 6, Patrick van Aanholt 7, Andros Townsend 7, Luka Milivojevic 6, James McArthur 6, Jeffrey Schlupp 7, Christian Benteke 6, Alexander Sorloth 6. The only thing is that has saddened me today is the fact we've gone home with no points.
It seemed Palace had done enough to hold off United's advances and clinch a draw, but Matic stepped up in stoppage time, lashing in his first goal for the club from long range to clinch an unlikely victory and put Mourinho's side back up to second ahead of Saturday's clash with Liverpool.
"But I have to say Roy had an incredible gameplan, really aggressive. sometimes the victor is the one that deserves congratulations but I think many times on the loser's side I did many things right and I think Roy did everything right", Mourinho praised his counterpart.
"There's not been many games where we've come back - granted, there's not many games when we've gone 2-0 down".
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Palace had failed to win any of their previous 17 Premier League fixtures against United, scoring only five goals during that run, but set about rectifying that statistic with an 11th-minute opener.
United manager Jose Mourinho described his team's defending for that goal as "disgraceful, childish". A clear leap from last year's securing of fourth place on the last day of the season.
"After 2-2, in some games, you would probably take that at 2-0 down but we went after them and it's great".
'We need to do more for sure - we drop some important points in small games. "If we had drawn the game - I don't think anyone, Jose included - would have said it was a scandal", he said.
With runaway leaders Manchester City closing in on their third league title in seven seasons, attention has shifted to the fight for Champions League qualification and United's battle with Liverpool to finish second behind their neighbours.
Matic's goal capped a relatively decent personal performance from the Serb, who is looking like returning to the form he showed just after signing for the Red Devils.