Sanchez has been replaced by rookie Geno Smith in the Jets' lineup and the 22-year-old has guided them to a 3-2 start in the 2013 season.
Sanchez said in statement: "After over seven weeks of hard work and intense rehab, I've been advised by Dr. Andrews and other doctors that my shoulder injury clearly needs to be addressed surgically.
"I'm very disappointed that I can't be out there to help my team on the field, but I'll continue to help our team in whatever capacity I can.
"I want to thank Dr. Montgomery, Dr. Andrews, Dr. Burns and Jets trainer John Mellody for helping me through this process and advising me along the way. All doctors expect a full recovery and I look forward to getting back on the field. Until then, Go Jets!"
The 26-year-old was drafted fifth overall by the Jets in the 2009 Draft.