The centre-back sat out PSG’s last two league games with an unspecified injury, and is said to have trained separately from his team-mates on Friday due to the problem.
It was hoped the Brazil international would have regained his fitness in time for the cup final, but he has now confirmed on Instagram that he will be unable to take part in the game at Stade de France.
"Unfortunately, I will not be on the pitch today! But the heart will be with you, PSG," the 34-year-old wrote.
Silva’s omission is a blow for Thomas Tuchel’s side, but means Presnel Kimpembe will likely be given the opportunity to start alongside Marquinhos at the heart of defence.
The PSG captain has played 39 times this season, with 25 of those appearances coming in the league.
Despite the setback to Silva, there is good news surrounding his international team-mate Neymar, who has has been tipped to start in the cup final.
PSG are looking to complete a domestic treble on Saturday, having already won the Trophee des Champions and Ligue 1 this season.
Should the Parisians achieve such a feat, it will be the second year in a row they have achieved the treble.
While PSG have romped to the top of the table, they have struggled in recent weeks and dropped points in three consecutive games, blowing the chance to secure the Ligue 1 crown on each occasion.
On the fourth time of asking, PSG did guarantee top spot in the table for the 2018/19 season by beating Monaco 3-1.
While domestically the season has been a success, Tuchel will have been left disappointed with another substandard Champions League campaign in which they were again knocked out in the last-16 stage of Europe’s elite competition.