Flores assured he has confidence in Ayala's professionalism.
"Of course I am going to use him," Flores told Spanish daily Marca. "He played here for many years, we all know him, he offered all of what he always had."
The veteran Argentinean centre back has agreed a two-year with Villarreal after playing for nine years at the Mestalla since leaving Serie A giants Milan in 1998.
Flores insisted he would not walk in the footsteps of Real Madrid coach Fabio Capello who decided to sideline David Beckham after the former England captain announced he will move to MLS side L.A. Galaxy at the end of the season.
He also said there was no pressure from Valencia’s management to keep the 33-year-old Ayala out of action for the remainder of his spell.
"There is not going to be an order from above telling me not to. Everyone here is committed to achieving our objectives,"
Ayala has won 107 caps for Argentina, taking part in two FIFA world cup tournaments, he was among the Albiceleste starting 11 in the friendly against France last Wednesday.