O'Connor suffered a thigh injury during the warm-up to Saturday's game against Sheffield Wednesday while Canavan has tendonitis.
Nigel Adkins, the Scunthorpe manager, is expected to give starts to the players who were limited to places on the bench against the Owls.
That would see Sam Slocombe, Eddie Nolan, Michael Raynes, Andrew Wright, Rory Coleman, Bobby Grant, Matt Godden, Michael Collins, Adam Boyes and Johnathan Williams come into the starting line-up.
Martyn Woolford played for 88 minutes on Saturday but may be given a decent runout against his former club.
The match kicks-off at 7.45pm at Bootham Crescent, with entrance £10 for adults and £5 for concessions. It is pay on the gate.