While the procedure is relatively minor - an arthroscopy to clean up stray cartilage - it has dashed the midfielder's hopes of an uninterrupted pre-season.
Lower had little trouble with his knee during last month's high-altitude training camp in Utah, but suffered the setback upon his return.
Despite initial concerns that the injury was worse, the 23-year-old should rejoin his teammates for training in January.
"They (the club medicos) thought it might be something that could keep me out for a few months. I'm so glad that it's not," he said.
"It's a minor hiccup, but I'd rather it now than in-season anyway.
"We've got great medical staff here so I'm confident they'll get me right."
Limited to 42 games in five years, Lower has been buoyed by the faith of the club after fearing the broken collarbone that ended his season would threaten his career.
Lower, who fractured his left leg in a NAB Challenge match against Hawthorn in March, made a mid-season return to the senior side only to suffer the collarbone injury against the Western Bulldogs in round 18.
He said that the assurance of coach Brad Scott had put his mind at ease.
"Whenever you do an injury, you always think the worst straight away," Lower said. "You have a couple of sleepless nights until you know what's going on.
"I was thinking, 'My luck can't get any worse'. Thankfully, Scotty was really good in letting me know that I would be here again next season.
"It's been a rough year, and now this. You start to dwell on it and start think, 'I've had a rough run the last couple of years'.
"I'm not kidding myself for a second. It's definitely a make or break year but I'll do everything I can to get another contract."
