Murphy came off Granny Red Shoes near the 650m mark and landed heavily, hurting his right hand.
After spending Saturday night in hospital, Murphy was diagnosed with ligament damage and he had hoped to avoid surgery.
Murphy's master Chris Anderson says doctors now believe surgery is unavoidable to ensure he has no problems in the future.
“Jackson will go under the knife on Tuesday and should be out for about six weeks,” Anderson said.
“He is aiming at being back in March and to be ready for the winter carnival which starts on Weetwood day in early April.
“He is also still keen to win the apprentices premiership.”
Murphy has ridden 17 metropolitan winners this season to be leading the apprentices title.