The bombs, planted in toilets on trains travelling the main railway line in Baluchistan province, went off within about three hours of each other on Friday. Eight other people were wounded.
A low-level insurgency by Baluch nationalists has gathered steam in the impoverished province this year, along with demands for more royalties from the country's main natural gas fields, located on their territory.
Railway police said the first bomb killed a soldier on a train from the provincial capital, Quetta, to the eastern city of Lahore at a station about 35km southeast of Quetta. At least five people were injured, two critically.
The second bomb went off on a train heading in the opposite direction about 100km southeast of Quetta, killing one person and wounding three.
Tensions in the region escalated on Thursday when tribesmen ambushed a troop convoy and fired rockets at a military base on the outskirts of Dera Bugti, 300km southeast of Quetta.
The ensuing 16-hour battle, in which the army deployed helicopter gunships, ended early on Friday after both sides agreed on a ceasefire, said a Frontier Corps spokesman, Lieutenant Colonel Rizwan Malik. He said eight soldiers were killed and 23 injured.
Major General Shujaat Dar, head of the corps, said 18 to 20 people from the Bugti tribe - the main tribe in the area - had reportedly died, and others were injured. He gave no further details.
Tribal fighting has escalated
It was the first public admission by any army or government official about tribal casualties in the fighting.
Abd al-Samad Lasi, a senior official at Dera Bugti, said on Saturday they had received reports from intelligence and security officials that more than 1500 armed men from the dominant local Bugti tribe had taken up positions in mountains outside the town and were waiting for an order to attack government installations.
A security official said paramilitary reinforcements were being sent to the region to support an already strong troop presence.
Lasi said government officials and their families started leaving the town on Saturday morning in vehicles escorted by paramilitary troops after receiving a warning from the chief of the Bugti tribe, Nawab Akbar Bugti, that he could not guarantee their safety.
"Yes, he has asked all government officials to leave Dera Bugti before 3pm today, and they are leaving with their families," Lasi said.
He said all 3314 officials and their families would leave Dera Bugti, which is about 50km from Pakistan's main gas fields.
Hundreds of supporters of ethnic Baluch nationalist parties demonstrated on Friday outside the provincial assembly in Quetta, protesting at what they said were high civilian casualties from Thursday's clashes.
Sardar Akhtar Mengal, an opposition politician and former Baluchistan chief minister, claimed the army had killed more than 50 innocent people, including women, children and minority Hindus. He accused the government of concealing civilian deaths.
A parliamentary committee has been set up to examine the tribesmen's claims for greater royalties from gas reserves, and other grievances. It is expected to make its recommendations to the government soon.