Defender Sergio Ramos sparked tension last week when comments he made about players’ commitment to the national team were taken by some as direct criticism of Costa and Fabregas.
The Chelsea pair are absent from the Spain squad that played Belarus in a Euro 2016 qualifier on Saturday and faces a friendly with Germany on Tuesday.
Following their 3-0 win over Belarus, Del Bosque said there may not be an automatic return for Costa and Fabregas when they are fit.
But he clarified his statement on Monday, saying he wanted to explain that there is strong competition for places in a new, youthful Spain side.
“I said that when someone comes in and does well then another who wants a place will find it more difficult,” Del Bosque told a news conference.
“If I say that Diego Costa and Cesc may struggle to play, I am not threatening them, nor is it a type of revenge or a reprisal against anyone. Simply it reflects a fact of football that everyone knows – if someone doesn’t play and his substitute does well, the other will have to do better in order to play.
“It is not a case that someone has been ruled out or won’t have a chance.”
Del Bosque feels that Spain – who failed to progress from their group at this year’s World Cup – are on the right track again.
Their victory over Belarus gave them nine points from four games in group C, three behind leaders Slovakia.
“It was an important win where we played well at times, especially in the first half,” he said.
Looking ahead to the Germany game, Del Bosque said: “In a game like this there isn’t much difference between a friendly and an official match.
“They want to maintain their high level and we want to continue the good line we have been in since the World Cup and improve our confidence.”
(Editing by Stephen Wood)