The 23-year-old will not face Casa Pia on Monday and has been removed from Benfica's preparations, with Newcastle United having agreed a €35 million deal for the right-back over the weekend.
Dedic had continued playing for Benfica while negotiations with Newcastle progressed, starting Thursday's 1-1 draw at Hearts with representatives from the English club watching on from the stands.
That changed by the time attention turned to Monday's fixture.
"Regarding Dedic, I can tell you that he will be out of the game," Silva said, explaining that the defender had previously remained available simply because the club's hierarchy had not yet instructed him otherwise.
"Without feedback from the structure, for me all the players count 100% for the games. They would be involved in the preparation and, therefore, I had no doubt that Dedic should start or be involved in the game."
That feedback has since arrived, with reports in Portugal stating documents have been exchanged between the clubs and a five-year contract already agreed with the player, who has since travelled to England ahead of his medical.
Silva made clear the departure was not one he welcomed from a footballing perspective, praising Dedic's performances last season and suggesting there remains plenty of room for the Bosnia international to develop further.
"It's obvious that he was a player that we, Benfica, didn't want to lose," Silva said. "The question of the offer and the financial aspect are things that Benfica's structure knows better than I do how to manage. That's not my role."
Those comments reflect the financial reality facing Benfica this summer, with the Lisbon club needing to raise funds from key assets and Dedic ultimately becoming one of them.
"Just as we want to sign players, there are also times when we lose players we didn't want to lose. The market is open and that's part of it," Silva added.
Dedic joined Benfica from Red Bull Salzburg for around €12 million last year and made 43 appearances in his debut season, contributing one goal and four assists. He remains one of several Salzburg academy products to have followed Matthias Jaissle to a new club in recent seasons, having previously worked under the head coach in Austria before Jaissle's move to Newcastle.