The Spain international scored his eighth goal of the season for the Blues in today's 3-0 victory over Aston Villa at Stamford Bridge, despite being restricted to minimal activity off the field.
Costa is likely to be called up to his national side later this month, although Mourinho believes that allowing the striker to rest for a fortnight would be the best choice in the long term.
"He cannot be on top of his game, but even so scoring a goal is good for his confidence," the Portuguese boss told talkSPORT. "He's doing almost nothing in training. He's just resting and recovering from the tight muscle he has. Every time he accumulates fatigue.
"I know a striker scoring goals is always nice for him and for his confidence, especially for a player like him who is not training as he should, because we are protecting him in certain situations.
"If he doesn't go to the national team and if he stays here 15 days just on treatment, he has the perfect chance to be top for Chelsea and top for the national team. If he doesn't have this period, will be always, plays one game, the other is in trouble, the muscle is tight, the muscle is danger to rupture."
Chelsea are currently top of the Premier League table.