According to the Serbian coach, Motshwari missed a late fitness test and was replaced by Musa Nyatama for the Telkom Knockout semi-final against Soweto rivals Kaizer Chiefs, a game the Buccaneers won 2-1.
Motshwari joined Pirates from Bidvest Wits before the start of the new season and has established himself as a regular in the team after being on the bench in the club's first two matches of the season.
"We played last Saturday friendly match against TTM [Tshakuma Tsha Madzivhandila]. He unfortunately got injured and we were a bit keeping to our chest and praying hard that he would come back. However, he could not pass the late fitness test," the former Ugandan national team coach said.
"He is our soldier that will still give us his best performances and it was unfortunate to play without a player who, arguably with consistency of matches, is one of our best top three performers in the matches behind us."
Micho continued: "Musa Nyatama came in after some period on the sidelines and he applied himself very well in the engine room. He and Xola Mlambo did very well and I believe our engine room worked very well today."
Pirates could have Motshwari back for their CAF Champions League game against Lightstars from Seychelles on Tuesday.