Meanwhile, fellow defender Darcy Gardiner is nearing his return from a similar injury for their cross-city rivals.
Ballard's knee had 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.
Gardiner is in the frame to play his first game either in the AFL or VFL for Brisbane since round eight last season after recovering from his own ACL tear.
The 29-year-old suffered the injury in round eight last year, joined by Lincoln McCarthy, Keidean Coleman, Darcy Gardiner and Tom Doedee - all sidelined with the injury.
Brisbane could also welcome back forward Charlie Cameron against West Coast on Sunday after he was withdrawn from their round-one clash against Sydney with calf tightness.
But they will be without Kai Lohmann (ankle sprain) and Brandon Starcevich (concussion) for at least one week.
McCarthy, who ruptured his ACL in the same match as Gardiner, will undergo surgery after re-injuring his right knee just days out from round one.
Doedee is expected to return within three to five weeks, though Coleman's timeline remains undetermined.
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