The Health and Safety Authority has launched a probed in to the incident at the former Point Depot site which is undergoing an £63 million transformation.
The men were taken to hospital but it is understood their injuries are not life threatening.
Three units of Dublin Fire Brigade, a specialist crews, ambulances and garda units rushed to the scene when the machinery overturned shortly after 8.30am.
One lane of traffic next to the quayside venue was closed during the incident, causing serious disruption in the area.
The HSA said it had launched an investigation.
The O2, which is part of the Point Village redevelopment in Dublin's Docklands, will hold up to 13,000 people.