"When there are changes it does have an impact on the cohesion of the team," he said after the draw at the Maracana that saw France progress to the last 16 as winners of Group E.
Deschamps made six changes to the team that hammered Switzerland 5-2 last Friday, including bringing in Southampton's Morgan Schneiderlin for his first international start in place of the banned Yohan Cabaye.
The draw against an Ecuador side that played most of the second half with 10 men after captain Antonio Valencia was sent off may have sealed France's qualification as group winners, but their performance was nothing like the spectacular showing against the Swiss.
"I have confidence in all 23 players and we needed to find the right balance between preserving some who have played a lot of games and making sure that others who we may require later on are in good condition.
"It takes away some of the fluidity and we were less dangerous in the first half. After the red card we had a bit more space and some good moves but were not as clinical in front of goal as usual."