Donald fired a level-par 71 on Sunday to finish on two-over par 286 for 72 holes, sharing 37th place, 16 strokes behind winner Carl Pettersson of Sweden.
Donald needed to share eighth place or better this week to keep his razor-thin margin ahead of McIlroy in the rankings. He finished six strokes adrift of that mark after matching his highest score in seven Heritage starts.
Once eight players reached the clubhouse ahead of him, Donald was ensured of giving the top spot back to McIlroy, whom he passed last month for the honor.
"Is it a concern? No," Donald said. "I would have liked to have played a bit more consistently this year. I built it up nicely last year through tournaments and winning a bunch.
"As a result there's a little bit of fluctuation in the world rankings now."
Donald, still seeking his first major title, first claimed the top ranking after winning last year's BMW PGA Championship on the European Tour.
"It's a lot more the focus the first time around," Donald said. "Now my focus is on winning tournaments."
Reigning US Open champion McIlroy, who turns 23 on May 4, claimed the top spot for the first time in his young career last month when he won the US PGA Honda Classic, ending a 40-week run by Donald.
But Donald moved past McIlroy two weeks later, reclaiming the top spot by winning the US PGA Transitions Championship.
McIlroy, who was off this week, is not expected to play again until the US PGA Wells Fargo Championship in May at Quail Hollow in Charlotte, North Carolina.
Donald will return to PGA play in two weeks at New Orleans starting April 26.