The club say it holds no grudges towards the Brazilian, while revealing Cristiano Ronaldo is being plagued by a back injury.
Madrid was keen to lure the Brazil international to the Spanish capital and saw an offer for the forward accepted by Santos at the weekend.
However, the 21-year-old has opted for a move to Camp Nou rather than Madrid and will sign a five-year deal with the Liga champion later on Monday.
"Neymar has chosen Barcelona and we have to accept that. We have nothing else to say," Pardeza told Canal+.
The Madrid director then went on to explain Cristiano Ronaldo's absence in the 3-3 Liga draw against Real Sociedad on Sunday.
"Cristiano has a problem with his back, in the neck area."
Real Madrid will end a disappointing 2012-13 campaign with a home match against Osasuna on Saturday.