FIFA issued guidance that all players picked for the Africa Cup of Nations should be released by their clubs seven days before each nation's first game, beginning on Dec. 15.
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Hosts Morocco are set to kick off the tournament against Comoros on Dec. 21, meaning that Mazraoui would have been able to play against Bournemouth had the game been scheduled for Saturday.
Instead, the fixture was moved into a broadcast slot on Monday night and fell within the FIFA release period.
Sources have told ESPN that United expected to have Mazraoui available and after their initial request was turned down by Morocco, club officials escalated the issue to FIFA.
FIFA sided with Morocco while citing their own release period beginning on Dec. 15.
United sources have told ESPN that the club feel they have been unfairly punished for having their game with Bournemouth moved to Monday -- a decision that was out of their hands -- and that Morocco have prioritised a training session over an important Premier League fixture.
Sources have told ESPN that Mazraoui was professional and respectful throughout the stand-off and spent the full week training with Ruben Amorim's squad before leaving for international duty late on Sunday.
In the absence of Mazraoui and injured defenders Matthijs de Ligt and Harry Maguire, Amorim was forced to field a makeshift defence against Bournemouth which included youngsters Leny Yoro and Ayden Heaven.
The game finished in a 4-4 draw.
Sources have told ESPN that both Bryan Mbeumo and Amad Diallo were allowed to play against Bournemouth after constructive talks between United and the federations of Cameroon and Ivory Coast, respectively.
The pair are now set to miss Sunday's trip to Aston Villa and Newcastle's visit to Old Trafford on Dec. 26.
