Stenson was appointed on March 15 and said he was fully committed to a role before signing with the Saudi-backed LIV Golf series.
Donald replaces Henrik Stenson after he was stripped of the role.
The American won the 3M Open in his previous outing.
The Swede was stripped of his role as Europe captain after joining the Saudi-backed breakaway tour.
The left-hander is currently sidelined by a knee injury and is not expected to play until next season,
The Swede lost the job 127 days after his appointment following his decision to join the LIV Golf series.
Homa has made no secret of his admiration for Woods.
Players who have resigned from the PGA Tour to join LIV Golf will not be eligible for next year’s Ryder Cup.
South Korea’s Ryu So-yeon climbed into outright second place on 15 under.
The tournament takes place at Wentworth in early September.
