The duo sat out training on Tuesday and Wednesday and England confirmed both players will return to their clubs.
Rose has been struggling with a groin complaint, while no reason has been given for McCarthy's withdrawal, although the issue is not thought to be serious.
Leicester City full-back Ben Chilwell may now get the chance to stake a claim for a place, with Manchester United's Luke Shaw having withdrawn from the squad last week.
England visit Croatia on Friday, before travelling to Spain – who defeated the Three Lions at Wembley last month – on Monday.
Tottenham will be hoping that the problem picked up by Rose does not keep him out of action for long, as they important fixtures approaching across multiple competitions.
Southampton have a similar run lined up in which they would prefer to have McCarthy available.
They have a derby date approaching, against Bournemouth, as well as a league meeting with Pep Guardiola’s City and a League Cup tie with Leicester.