"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. (Agencies)
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 could put out the same team every time but then it would be pointless having the other players here," said Deschamps.
"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,” he added.
"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,” he said.
However, Deschamps added: "It would need a lot more than that to spoil our satisfacton and our joy. We came here to seal our qualification and finish first, and we did it.”
"We didn't see ourselves as kings of the world after our victory against Switzerland. Every match is difficult. The World Cup is the highest level,” he said.
Meanwhile, Deschamps insisted that he has not seen a supposed elbow by defender Mamadou Sakho on Ecuador midfielder Oswaldo Minda, which upset his opposite number Reinaldo Rueda.
"I have not seen it. There were lots of challenges going in, which is part of the game too," he said.
"Even though I was on the French bench I didn't see it because it is sunk below the pitch,” he added.
Several leading European nations have already been knocked out of this World Cup, including holders Spain, Italy and England.
However, France are through to the knockout stage of a World Cup for the first time since their run to the final in Germany in 2006 and they will be favourites in the eyes of most to beat Nigeria in Brasilia on Monday.
Deschamps was not keen to discuss the meeting with the defending African champions, preferring instead to savour his side's qualfication but he did highlight their defensive strength.
"First of all I want to appreciate the fact that we are in the last 16, but as a team they are solid at the back and have a very good goalkeeper,” he said.
"They have quality going forward too so it will certainly be a difficult match,” he added.
Nigeria drew 0-0 with Iran and beat Bosnia-Hercegovina 1-0 before losing 3-2 to Argentina earlier on Wednesday.
"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.