The Serbian midfielder was suspended for the Wembley showpiece, which Chelsea won 2-0 to win the first trophy since Mourinho returned as manager ahead of the 2013-14 season.
However, the former Benfica man donned his kit to join his team-mates in celebration at the final whistle.
Mourinho said Matic hurt himself on the Wembley turf and would have missed Wednesday's 1-0 Premier League win at West Ham even if he was not serving the second match of his ban.
"I'm going to tell you something nobody knows, Matic is injured and he got an injury celebrating the cup. I'm not kidding," Mourinho said at his post-match news conference.
"It's not a big injury but if he wasn't suspended he wouldn't play. He twisted his ankle on the pitch."
Chelsea fans need not fear, though, as Mourinho confirmed Matic would train over the weekend ahead of next Wednesday's UEFA Champions League last 16 second leg encounter against Paris Saint-Germain.
The tie sits at 1-1 ahead of the Stamford Bridge fixture.
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