For the first time in the show's 43 years, the top prize - traditionally decided by ACM members - was determined Sunday through online voting. With the win, Chesney ties Garth Brooks and trails only Alabama, which won five in a row.
Chesney said immediately backstage that he thought fans should be included, just not by voting for the show's most important award.
Messages left for officials with the Academy of Country Music Awards were not immediately returned Sunday night.
Chesney was the night's leading nominee with 11, and ended up winning twice. His other win was for vocal event of the year for his work on the Tracy Lawrence hit "Find Out Who Your Friends Are."
Miranda Lambert won album of the year and Sugarland took single record and song of the year honors Sunday for their ballad "Stay".
"I'm sitting right behind Kenny Chesney and I just don't feel right taking this," said Lambert, who won for her sophomore outing, "Crazy Ex-Girlfriend." "I'm a songwriter, and I poured my heart and soul into this album. Thank you for appreciating it."
The win was big for Lambert, who beat out superstars Chesney and Brad Paisley, as well as hot new acts Taylor Swift and Rodney Atkins.
Members of Sugarland acknowledged that "Stay" wasn't exactly the kind of song that was created for commercial or awards success.
"Thanks everybody for believing in a song that's almost a five-minute acoustic song," Kristian Bush said. His partner, Jennifer Nettles said, "It means so much to me that you guys really relate to this song."
Jack Ingram won top new male vocalist. The 37-year-old Texan released his first album in 1992 and bounced around a number of record labels before his career took off.
"Sometimes it takes a long time and that's my story," Ingram said backstage. "I put in a lot of hard miles, and I'm thankful."
Lady Antebellum took home top new duo or vocal group. "Does this mean we get to hang out with Kenny Chesney now?," the trio's Charles Kelley joked.
Swift won top new female vocalist. The 18-year-old thanked her mother for going on the road with her beginning when she was 16, leaving behind a comfortable life to sleep in rental cars and on airplanes so her teenage daughter could pursue her dream.
"Mom, thank you so much," she said as she fought back tears. "I love you. This is for you."
Earlier, Brad Paisley's "Online" won video of the year. It was produced by former "Seinfeld" star Jason Alexander, who also co-starred and made an onstage appearance Sunday night, joking that he didn't believe the stereotype of country stars and fans being religious - seeing as he hadn't spotted any of them at synagogue.
Tracy Lawrence won vocal event of the year for "Find Out Who Your Friends Are" with Tim McGraw and Chesney.
"This is absolutely awesome," Lawrence said. "We moved a big mountain pulling this off."
Hosted by Reba McEntire, the awards were aired live from the MGM Grand.
Carrie Underwood opened the show with a saucy performance of "Last Name," a song about waking up and finding herself married to yesterday's drunken one-night-stand. She wore a simple white jumpsuit with a wide rhinestone belt and held an equally bedazzled microphone to match.
In contrast, it looked for a moment like Swift was going for an Avril Lavigne vibe as she started her performance of "Should've Said No." She wore a hoodie sweatshirt and jeans as she accompanied herself on an acoustic guitar.
A few minutes into the song, two male dancers ripped off her jeans and hoodie in one swipe to reveal a little black dress. She finished the number with rain pouring down on her from an on-stage water feature.
"Dang, I wanted to go in the water," said Kix Brooks after Swift finished her song. "Taylor gets to have all the fun."
Strait, who was celebrating his 56th birthday, performed his 56th No. 1 hit: "I Saw God Today."
Other musical performances included Paisley singing "I'm Still A Guy," Lambert with "Gunpowder And Lead", Toby Keith performing "She's A Hottie" and Chesney singing "Better As A Memory."
It was McEntire's 10th time as host, going back to 1986. In those days, she joked, "Underwood was a typewriter, Sugarland was doughnut shop and a Pickler was someone who made pickles.
"Back then, Roger Clemens wasn't even interested in country music," she cracked. Clemens recent acknowledged a long-standing relationship with country singer Mindy McCready that began when she was 15. The former baseball player maintains the relationship was not sexual.
Chesney led all nominees at the awards show with 11, including the night's most coveted trophy, entertainer of the year.
Other leading nominees were Rodney Atkins with six, and Brad Paisley, Big & Rich and Sugarland with four apiece.