Jackson also won for male vocalist and album of the year for "Drive." His Sept. 11-themed "Where Were You (When the World Stopped Turning)" won for single and song of the year.
Typically a man of few words, Jackson found himself in front of the winner's microphone numerous times throughout the show.
"I'm sorry, y'all, I keep coming up here," Jackson said as the audience gave him a standing ovation for single of the year.
"It's been uplifting and humbling at the same time. I'm just a singer of simple songs, and that's the truth," he said, quoting a line from the song.
Martina McBride -- whose hits include "Blessed" and "Independence Day" -- was named female vocalist of the year for the second time in her career.
"I was happy with one," a teary-eyed McBride said backstage. "I never expected to win again."
Rascal Flatts -- whose album "Melt" landed at No. 1 on the Billboard country albums chart Wednesday -- won the Horizon Award, presented to an artist or group that the CMA believes will have a successful long-term career.
Dixie Chicks won for best vocal group, but they were not in Nashville to accept their fourth CMA Award in the category. Natalie Maines, Martie Maguire and Emily Robison were in Texas, awaiting the birth of Robison's first child, according to a CMA spokesman.
Brooks & Dunn won for best vocal duo -- their 10th CMA Award in that category in the last 11 years.
The CMA Award for vocal event of the year went to Willie Nelson and Lee Ann Womack for "Mendocino County Line."
Veteran dobro player Jerry Douglas was named musician of the year.
Brad Paisley's "I'm Gonna Miss Her (The Fishin' Song)" won for best music video. The video -- directed by Peter Zavadil -- features talk show host Jerry Springer, sportscaster Dan Patrick, country music legend Little Jimmy Dickens and actress Kimberly Williams, Paisley's fiancée.
Hosted for the 11th straight year by Vince Gill, the 36th Annual CMA Awards were televised live on CBS.