Last Saturday's explosion carved out a 60cm crater near the shrine in the town of Fatehpur in Baluchistan province, where 20,000 people had gathered for a three-day event marking the anniversary of the death of a 19th century Shia cleric.
No one has claimed responsibility for the time bomb blast.
Pakistan has a history of sectarian violence between extremists of both the majority Sunni and minority Shia sects.
According to the local police, the toll rose on Monday from 30 to 46 after five people died overnight of their injuries.
Also, 11 people whose bodies were picked up immediately after the blast were not initially counted in the death tally, district police chief Khadim Husain said.
Explosives experts pored over pieces of metal collected at the blast site to try to determine what kind of bomb was used, he said.
"Police officers have also asked the caretaker of the shrines questions about why the shrine might have been targeted or who might be behind it," Husain added.
Meanwhile, UN Secretary-General Kofi Annan has condemned the attack "in the strongest terms" and called for restraint among those who might want revenge.
"No cause can justify terrorist attacks anywhere"
UN Secretary-General Kofi Annan
He said "no cause can justify terrorist attacks anywhere".
"The secretary-general calls for those responsible to be brought to justice and appeals for calm and restraint in the face of this brazen and cowardly act," UN spokesman Fred Eckhard said in New York.
A bomb packed with about 3kg of explosives went off among pilgrims on Sunday as they took supper in an open area about 150m from the shrine.
Later on Sunday, frightened pilgrims crammed into buses leaving the remote village, about 800km southwest of Islamabad, as relatives sifted through bloodied caps and shoes for signs of loved ones.
Others congregated at a hospital in a nearby town where most of the bodies were collected.
The attack added to security fears in restive Baluchistan province, hit last week by fighting between government forces and tribesmen.
Pakistan has been plagued with attacks by fighters angered by President Pervez Musharraf's support for the US-led war against al-Qaida and the Taliban in neighbouring Afghanistan.