Ms Baloch, a controversial figure known for her outspoken posts and suggestive photos and videos, posted selfies with Mufti Abdul Qavi last month.
He was suspended from two important councils as a result.
Ms Baloch, 26, was strangled by her brother Waseem early on Saturday in their hometown of Multan.
He admitted the apparent "honour killing", saying it was justified.
The cleric has denied any role in the murder but says he will appear for questioning if summoned by police.
Following the murder he said Ms Baloch's fate should serve as a lesson for others who want to mock religious figures.
He also said that he had "forgiven" her.
Police in Multan say they are also investigating Ms Baloch's other brother, Aslam, a junior army officer whom her father accused of encouraging Waseem to murder her.