Police said those killed were the driver of the passenger train and a female passenger. One of the injured is in a serious condition, AP reported.
Markus Trieb, a spokesman for northern Swabia police, said Tuesday that the passenger train was traveling from Augsburg to Ingolstadt when it hit the cargo train near a station in the town of Aichach.
He said the driver of the cargo train was uninjured. Authorities are investigating the cause of the crash.
In a separate incident in Bavaria, two people were killed Monday when a train hit their car at a crossing near Lake Starnberg.