Captain and key centre-back Ramos sustained a cut in the scoreless draw with cross-city rivals Atletico Madrid at the weekend and was subsequently left out of the 20-man travelling party picked to visit CSKA Moscow.
But while Gareth Bale, Isco and Marcelo are all unavailable through injury, Ramos' omission is purely with a view to preserving his fitness for the season ahead.
The 32-year-old's exclusion presents another hurdle for the Champions League holders as they seek to move on from a two-game winless run in La Liga.
"Ramos hasn't travelled because he has played about 120 minutes more than his team-mates," Lopetegui said.
"We're looking at this as a marathon, the whole season, the bigger picture. Another player can come in and play his position.
"That's my job - to sit in this seat and make these kinds of decisions."
Madrid have only taken four league points from a possible nine since starting their Champions League title defence with a comprehensive win over Roma last month.
The stalemate against Atleti was their second blank in as many outings, but Lopetegui believes the result offered no cause for concern.
"It was a very tough demanding game against a tough opponent," he added.
"We had one less day to prepare for the game. I think overall there were plenty of positives. Of course there were a couple of setbacks but we showed we had players who can come in and play well.
"Unfortunately we couldn't get that goal. We just need to keep generating the most chances possible and hopefully put them away. I'm sure the ball will go in."