Lukaku had earlier ballooned a shot over the crossbar with the goal gaping but reacted smartly to steer the ball home after Matic's effort had been parried by Keylor Navas.
Matic believes the 24-year-old will have had his confidence boosted by his goal and expects him to hit the ground running when the Premier League begins this weekend.
"It's very important for us that our strikers score goals," the midfielder told MUTV. "It's very important for confidence.
"As you know, he missed a very good chance but this can happen – it's football. But I am happy for him that he scored a goal after that and I'm sure that he will continue to score goals and that he will score many this season."
Jose Mourinho's side were largely second-best in Tuesday's encounter in Skopje, with Casemiro and Isco having given Madrid a deserved two-goal lead before Lukaku offered some late hope of a comeback.
Champions League (@ChampionsLeague) August 8, 2017
Matic was frustrated with the result but has called on United to turn their full focus to Sunday's league opener against West Ham.
"We tried everything to equalise and then to win the game," said the former Chelsea man. "But they are very experienced and they also had some chances to score another because at the end we tried to go with everything to score and they had some counter-attacks.
"On Sunday, we have a very important game at Old Trafford in front of all our supporters. We have to rest and to be ready for West Ham."