The toll from the crash, which occurred in Sindh Province, rose to 56 after bodies were retrieved overnight from mangled coaches strewn across the tracks, Pakistan Railways spokeswoman Nazia Jabeen told Reuters.
An earlier estimate put the death toll at 41.
One side of the two rail tracks has been cleared and work was in progress to clear the other one to help restore traffic.
"We saw a terrifying scene here," said resident Sher Mohammad. "We brought water, picked up children. Passengers who were coming out of the train were mostly in agony."
The trains were carrying a total of 1,388 passengers.