The Argentine was rushed back to face Bayern on Tuesday and put in a toothless performance as Barcelona lost 4-0 at the Allianz Arena.
The Argentine's participation in the Allianz Arena clash had been in doubt right up until just a couple of hours before kickoff, with the 25-year-old having failed to feature for the Blaugrana in all but one game since sustaining a hamstring injury against Paris Saint-Germain on April 2.
The Catalans eventually slumped to a 4-0 loss, with Messi putting in a disappointing performance, and Minguella believes he was not fit enough to feature.
"His father told me at lunch that he was not able to play," the agent-turned-pundit is quoted as saying by Marca.
Barcelona will be hoping that Messi is fully fit when the club meets Bayern again in the second leg at Camp Nou on May 1 as the team looks to produce an unlikely comeback.
Barcelona travels to Athletic Bilbao on Saturday.