Friday's announcement came as Bhutto was buried in her ancestral village in the province of Sindh against a backdrop of continued violence, with the death toll from disturbances rising to 31.
Cheema also said Bhutto had died from injuries caused by hitting her head on her car's sunroof as she came under fire, rather than from bullet wounds or shrapnel.
Earlier reports said Bhutto was gunned down by an assassin.
The assassin then blew himself up in an attack that killed a total of 16 people at the end of an election campaign rally in Rawalpindi on Thursday.
While pointing the finger at al-Qaeda, Cheema said Mehsud was also behind a suicide attack on a Bhutto rally in October that left 140 dead.
Pakistani authorities say Mehsud is based in the tribal region of South Waziristan.
'Pack of lies'
Cheema's claim that Bhutto's death was not caused by bullet wounds but by head injuries was described as "a pack of lies" by an aide of the slain politician.
Farooq Naik, a senior official in Bhutto's Pakistan People's Party (PPP), said: "Two bullets hit her, one in the abdomen and one in the head.
"It is an irreparable loss and they are turning it into a joke with such claims. The country is heading towards civil war."
Kamal Hyder, Al Jazeera's Pakistan correspondent, said people were asking why the car in which Bhutto was travelling was not damaged by the fatal attack.
"A lot of people in Pakistan believe there may be some kind of conspiracy behind the assassination," he said.
Questions have also been raised as to why the scene of the attack that killed Bhutto was hosed down by the authorities soon after the blast, a move that may have destroyed valuable evidence.
Earlier on Friday, hundreds of thousands of mourners gathered for Bhutto's funeral in front of the mausoleum in Garhi Khuda Bakhsh, a village 5km from the Bhutto home in the town of Naudero in Larkana district.