Houston announced the decision on Saturday evening, the deadline for underclassmen to declare.
In a statement released by Georgia, the junior from Statesboro thanked the school and head coach Mark Richt, without whom Houston said "I would not be where I am today."
"It was a very hard decision to make but in the end, I had to do what's best for my family and me," Houston said. "Thanks to all of the fans who were behind us the whole time I was in Athens."
Richt suggested several times over the past few months that Houston could improve his stock by returning for his senior year. Right now he's projected to go anywhere from mid-first round to second round.
"Justin is a great person and great player and we'll miss him," Richt said in the statement. "He's been an integral part of our team the past three years. We wish him nothing but the best as he moves into this next phase of his football career and I'm certain he'll be successful."
The news means Georgia lost two players early to the NFL draft: Star receiver A.J. Green declared on Sunday, and is expected to be one of the top picks in the draft.
As for Houston, his status is a bit more unknown. Listed at 6-foot-3, 258 pounds, he could play outside linebacker or defensive end in the NFL. He will likely be eyed by teams that run a 3-4 defense, since he flourished in that system in 2010 at Georgia.
Georgia will now be without its two top playmakers from a defense that finished the season ranked fourth in the SEC in total defense and seventh in scoring defense. Inside linebacker Akeem Dent, who led the team in tackles, was a senior.
Those four linebackers started a total of 36 games this year, accumulating 289 tackles, 14 sacks and 32.5 tackles-for-loss.
But two players who sat out this year got good reviews in practice: Jarvis Jones, the Columbus native who transferred from Southern California, and Richard Samuel, the converted running back. Both will be eligible in 2011.
Houston finished the regular season as the SEC's leader in sacks, with 10. He was a first-team All-SEC pick by the AP and the coaches, and was a finalist for the Bronko Nagurski and Butkus awards.
The Statesboro High School graduate finishes his career with 20 sacks and 38 tackles-for-loss. He also had one interception – on his final play at Sanford Stadium, to seal Georgia's 42-34 win over Georgia Tech.