DC returned to Major League Soccer action for a new season on Sunday with a dramatic 3-2 win over Toronto.
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Morrison, who was a Manchester United player at the same time as Rooney, did not feature in the game.
The midfielder was only signed in the summer, but the DC boss has revealed the reason why the 30-year-old is not in his squad.
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Rooney said: "I felt with players we were bringing in and different things you need to look at in terms of the budget, international slots, etc, it was more important I got different players in for different positions, which we felt were more important to me."
Morrison signed a professional deal at United in 2010 but only made three senior appearances for them before leaving in 2012.
He never shared the pitch with Rooney during his time at Old Trafford though, signing for West Ham after his departure.
The midfielder then went on loan to Birmingham, Queens Park Rangers and Cardiff before making a permanent switch to Lazio.
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After further loan spells and moves across Europe, Morrison was reunited with Rooney at Derby County in 2021 when the latter was the manager.
He featured heavily at the then-Championship side last season, scoring four league goals in 36 appearances.
Just days after Rooney was appointed at DC, Morrison also joined the club and has featured 14 times for them so far.
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However, even though he is still able to train with the squad, he won't be making any MLS league appearances this season.
Morrison was once considered one of football's top rising talents, but the recent news comes as another setback for him in his career.
It remains to be seen what the future now holds for him, with his appearances at DC likely to be limited this year.