Boonen, who became the first cyclist ever to win the Flemish cobblestone quadruple of E3 Harelbeke, Gent–Wevelgem, Tour of Flanders and Paris–Roubaix in the same year in 2012, fell whilst training on his mountain bike on January 13 and bacteria penetrated through a small cut.
The 32-year-old said: "I fell on my left elbow. I didn't even think about it, it was just a little scrape to the elbow, which I cleaned and disinfected once I got back home.
"During the week everything was going well, I wasn't having any problems. Then suddenly on Saturday my elbow started swelling. The following morning I went back to the hospital for a check up. When the doctors saw how swollen my arm was they immediately decided to operate.
"I have to thank the medical staff who understood right away that the infection was spreading."
The 2005 world champion will now spend a few days in hospital but hopes to get back in the saddle soon before the spring Classics.
"Next week I'll be thinking again on my training and competitive schedule. Of course, this problem couldn't have come at a worse time, what with the upcoming Classics," he added.