Prado was injured in the Braves' 2-1, 11-inning victory over the Florida Marlins on Monday night while swinging at a pitch in the fifth inning.
"It's bad news. He's got two problems," Braves manager Bobby Cox said following Tuesday's 3-2 win over the Marlins.
"It's a big blow, but we can't use it as an excuse," Atlanta pitcher Tim Hudson said.
The rehabilitation requires two months of complete rest (no activity) and with normal healing, Prado could begin preparations for spring training.
Prado said he originally injured himself on a diving catch in the fourth inning, then aggravated it when he swung in the fifth.
Prado said after he swung, he heard a pop and couldn't run.
Prado finished an all-star season with a .307 batting average, 15 home runs and 66 RBIs.
Prado began the season as Atlanta's everyday second baseman but took over at third base after Chipper Jones suffered a torn ACL.
With the Braves in the thick of the NL wild-card race, they will turn to Brooks Conrad to fill the void at third base.
Conrad had an RBI triple and scored on Eric Hinske's two-run homer for Atlanta on Tuesday.
"I wish I could have gotten some more hits earlier in the game," Conrad said. "Obviously Prado going down wasn't what I was looking for."
Information from ESPN The Magazine's Buster Olney and The Associated Press was used in this report.