There has been some speculation Rose has been omitted because he was subjected to racial abuse in Serbia, while playing for England U21s two years ago.
Spurs kick off their Group C campaign in Belgrade on Thursday evening with emotions still raw from the European Championship play-off 120 miles south in Krusevac.
A mass confrontation on the pitch marred England Under-21s' progress to the finals in October 2012, when Rose, at the time on loan to Sunderland, was sent off for his reaction to racist abuse.
Nikola Ninkovic was banned for a year by the Serbian Football Association for his part in the melee and claimed in the immediate aftermath that Rose provoked home supporters with "inappropriate gestures".
Recently-appointed captain Younes Kaboul, Emmanuel Adebayor, Mousa Dembele and Nacer Chadli have also stayed at home, but Pochettino is playing down the situation ahead of the match.
"No, it's not for that reason that he did not come," the Argentinian said.
"I know about the problems two years ago but they are not the reason he is not here now. We know the situation but it is not the reason. He didn't ask to be left out.
"The decision was based on football only. All my selection decisions are based on football always.
"I think two years ago is a long time. My decision was simply to give him a rest because down to him being tired after Sunderland.
"Before that he was with the national team for two weeks. It's always a stress to go with the national team.
"We also have a big squad and it allows other players to play and for me to see another player."