Musharraf, who ruled Pakistan from 1999 to 2008, has also been charged with ordering a military raid on the Taliban-linked Red Mosque in Islamabad during his term.
He dismissed all charges as politically-motivated and said in Dubai Saturday that he would defend himself in courts on return.
Musharraf's Emirates flight from Dubai landed at around 12:45 pm after a journey that saw his official Facebook and Twitter accounts provide a running commentary, posting messages and photographs of him on board.
“Settled in my seat on the plane to begin my journey home. Pakistan First!” said one message posted on the @P_Musharraf Twitter account, with a picture of him wearing an off-white, traditional salwar kameez outfit.
Some of his supporters on the flight shouted “Musharraf zindabad”, annoying other people among the regular passengers.
Musharraf was forced to cancel plans to address a public rally at the Karachi mausoleum of Pakistan's father of the nation Mohammad Ali Jinnah.
Meanwhile Bhutto's son Bilawal Bhutto Zardari, who is chairman of the Pakistan People's Party, has accused Musharraf of her murder.
In 2010 a UN report said Bhutto's death could have been prevented and accused Musharraf's government of failing to provide her with adequate protection. His administration blamed the assassination on the Pakistani Taliban.
