In automated container terminals (ACTs), quay cranes (QCs), automated guided vehicles (AGVs), and automated yard cranes (AYCs) interact intensively to handle containers at seaside and yard side. This work investigates interacting equipment in ACTs that employ AGVs with the capability of lifting a container temporarily buffered at the transfer area in front of a storage block. By establishing and using the Petri net model of equipment interaction system (EIS) for container transportation, deadlock control problem is studied for handling operations in ACTs, where all QCs, AYCs, and transport vehicles are considered as system resources. Deadlock is characterized as maximal special circuits (MSCs) that are saturated at a system state. After a deadlock detection method through MSC enumeration in the system Petri net model is developed, a procedure is proposed to resolve deadlock situations where an AYC is involved in the corresponding circular waiting relations. By modifying the operation sequence of AYCs, the procedure can resolve the conflicts among concurrent processes so as to eliminate deadlocks. Examples are presented to illustrate the effectiveness of the deadlock handling method, which is also tested in a simulation study. Results show that the EIS can recover from detected deadlocks involving AYCs to ensure smooth transport operations of container jobs.