Rashford had his most impactful first 45 minutes of the season in Portugal, scoring the opener before setting up Rasmus Hojlund, but he was replaced at the half-time interval, seemingly due to an injury.
However, Ten Hag confirmed after the match that it was a tactical decision to withdraw the England international, with the Red Devils having another game on Sunday afternoon against Aston Villa.
The 26-year-old was in the starting side against Unai Emery's team but was withdrawn in the 64th minute of the 0-0 draw.
Rooney has hit out at the "crazy" decision to substitute Rashford, who struggled to make his mark during the 2023-24 campaign after an outstanding 2022-23 season at Old Trafford.
Rooney bemused by Ten Hag's Rashford substitution vs. Porto
"Some of the changes he is making, you never see top teams changing their centre-backs during the game - or the back four - and that happens on a regular basis," Rooney told the Stick to Football podcast.
"The Rashford one, that was the best I've seen him play [vs. Porto] for a long time and to take him off at half-time and say we've got another game at the weekend is crazy.
"I guarantee on this international break you see videos of him training with a coach away from the training ground - so if he can't do two games in a week, he should have been resting."
Rashford has only scored once in the Premier League this season, with his strike coming against Southampton in the middle of September, and he has since drawn blanks against Crystal Palace, Tottenham Hotspur and Villa.
Will Rashford start against Brentford?
Having again been left out of the England squad for their October internationals, Rashford should be fresh for Man United's next game against Brentford on October 19.
The forward has started six of Man United's seven league games this term, and he will be bidding to add to the four goals that he has scored in all competitions in 2024-25 when the Bees visit Old Trafford next weekend.