The defender who was signed from Ajax this summer hurt himself while tackling Brennan Johnson late in the first half. Although he went on to start the second half, he quickly pulled up and limped off in the 50th minute.
Arsenal have now revealed the full extent of the problem.
A club statement said: "Further to detailed assessments with consultant specialists since Saturday, we can confirm that Jurrien Timber has sustained an injury to his anterior cruciate ligament in his right knee.
"Jurrien will undergo surgery in the coming days and will be out of action for a period of time.
"The support and expertise from our medical team and everyone at the club will now be focused on Jurrien’s rehabilitation programme, to ensure he recovers well and is back playing as soon as possible."
Timber wrote on Instagram: "Gutted to share my injury is more serious than expected, especially after the warm welcome I've received.
"I wanted to repay you on the pitch, which will not be possible for the forthcoming period. I'm blessed with a lot of great people around me, together we will do anything to get back as soon and strong as possible.
"For now I'll be supporting our team from the stands of course."