Blake Shelton was the only multiple winner at the fan-voted awards, picking up male video of the year for Who Are You When I'm Not Looking and best web video for Kiss My Country Ass.
While his wife, Miranda Lambert, won female video of the year for her hit song, The House That Built Me.
Kid Rock hosted the Nashville ceremony.
Swift accepted her award via satellite while on stage in Wisconsin, where she is on tour.
"I wish I could be there, but I'm hanging out with 15,000 of my closest friends in Milwaukee," she said.
The singer opened the ceremony in a pre-recorded video parody of the film Thelma and Louise with fellow country star Shania Twain.
The show also featured performances from Sheryl Crow and Kid Rock, Lady Antebellum, Keith Urban and Jason Aldean, who sang a surprise version of his hip hop-infused hit Dirt Road Anthem with rapper Ludacris.
Other winners included Sugarland, who won duo video of the year for Stuck Like Glue, and Lady Antebellum's Hello World, which was named group video of the year.
Teen star Justin Beiber also picked up his first country award, winning the collaborative video prize for That Should Be Me with Rascal Flatts.
The Zac Brown Band and Jimmy Buffett won the CMT performance of the year video, for a version of Margaritaville which was broadcast on CMT in March.
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