Rose was subject to racial abuse while playing for England's Under-21s two years ago in Serbia.
The left-back was sent off during the game due to his reaction to the abuse, which was condemned by the Serbian Football Association.
"No, it's not for that reason that he did not come," Pochettino told Sky Sports News.
"I know about the problems two years ago but they are not the reason he is not here now.
"The decision was based on football only. All my selection decisions are based on football always."
Tottenham travel to Serbia to face Partizan Belgrade in the Europa League on Thursday night.