Mr. McDonald, of Fresno, was 62 years old.
Audra McDonald will miss the May 2-3 performances of Broadway's 110 in the Shade due to the sudden death of her father, a spokesman for Roundabout Theatre Company confirmed. She will perform in the musical May 1 at Studio 54 and resume performances May 4.
The Fresno Bee reported that Mr. McDonald retired in 2005 as the assistant superintendent of human resources for the Fresno Unified School District.
Stanley McDonald was serving in the U.S. Army and stationed in Germany at the time of Audra's birth in 1970. She and younger sister Alison grew up in Fresno.
He was reportedly an experienced helicopter and fixed-wing pilot, and had built the craft himself. The crash is being investigated by The Federal Aviation Administration and the California Highway Patrol.
In recent weeks, Audra McDonald has been playing Lizzie in previews for the Roundabout Theatre Company's new production of the musical 110 in the Shade, scheduled for a May 9 opening.