The Portuguese is considered to be a hindrance in Rashford's development by some, as he has dipped in and out of the starting XI at Old Trafford, struggling to hold down a consistent first-team place.
This has led some commentators, such as former England defender Jamie Carragher, to suggest the 20-year-old needs to leave the Red Devils if he is to fulfil his potential.
Southgate, however, has reassured supporters that the young attacker, who scored the only goal of the game as England beat Switzerland 1-0 on Tuesday, is rated by his club boss as much as anyone else.
“Jose thinks the world of Marcus,” he said. “He's a huge admirer of him, but he has got his job to do. There is huge competition for places at his club so you can understand that.
“I understand the difficulties that club managers have. They have to try and win matches. They have to rotate their squads.
“It's not my business to interfere with club managers. They have a difficult job to do and they have big squads at the top six, with huge competition for places.”
Southgate is confident that Rashford’s spell away with England will have raised his morale, as he also netted in the 2-1 Nations League defeat against Spain on Saturday.
“We really wanted to make Marcus feel important over this period,” said Southgate.
“It was important especially to get him in the penalty box and remembering the areas he needs to be scoring goals from.
“His confidence will be boosted I'm sure, with two goals against top-quality opposition.”
Rashford will go back to United and compete for a starting berth against Watford on Saturday with the likes of Romelu Lukaku, while the Red Devils will play a Champions League match against Young Boys in Switzerland the following Wednesday.
He has played in three of four Premier League matches for his side this season, but has yet to find the net or make an assist as the Old Trafford side have kicked off with two wins and two defeats.