The Gold Coast defender's knee buckled after an awkward landing late in the second quarter of their 87-point round-one win over West Coast.
Suns coach Damien Hardwick refused to fear the worst for Ballard following Sunday's match, before scans on Tuesday confirmed the extent of the injury.
It was Ballard's first game of the season after their Opening Round fixture against Essendon was postponed due to Cyclone Alfred.
He had overcome an ankle injury to play against the Eagles.
"It's terrible news for Charlie and the team, but we will provide him with all the support he needs throughout his recovery to ensure he returns to his best next year," Suns football performance boss Wayne Campbell said in a statement.
"Charlie is an extremely important member of our club, on and off the field, and we will be with him each step of his journey."
It is a massive blow for the Suns in their pursuit of a maiden finals series.
The 25-year-old tall is an integral part of their defence, having played 23 matches in each of the past two seasons.
Ballard joins Mac Andrew (chest), Sam Flanders (back), Leo Lombard (shoulder) and David Swallow (knee) on the sidelines.
Gold Coast are at least hopeful of welcoming back Andrew and Flanders after their round-two bye.
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