"The last trapped victim has been extricated after four hours by cutting thick metal sheets of train cartridge with the help of hydraulic cutters," a provincial emergency service, Rescue 1122, said in report.
It said four people had been killed. Earlier, media put the death toll at six with more than 150 injured.
Pakistan's colonial-era railway network has fallen into disrepair in recent decades due to chronic under-investment and poor maintenance.
About 130 people were killed in July 2005 when a train rammed into another at a station in Sindh province, and a third train hit the wreckage.