al-Mirghani, leader of the main faction of the Democratic Unionist Party (DUP), one of Sudan's most significant blocs, and the large Khatmiya Sufi sect, was met by thousands of followers beating drums at Khartoum's main airport.
In a filmed statement released on Wednesday, the elderly al-Mirghani rejected a hasty agreement and foreign intervention in the political crisis, and assigned Jaafer with closing ranks in the party as his deputy.
"Hasty steps in the wrong direction and the rush to offer solutions before their time can bring about great harm," he said, recalling past experiences of foreign-brokered agreements.
al-Mirghani has been based in Egypt for about a decade and his arrival follows military leaders and the former ruling Forces of Freedom and Change coalition saying they had reached understandings including the military's exit from politics.
The DUP has a strong support base in rural areas of Sudan but has lately been embroiled in a struggle between al-Mirghani's two sons - Jaafer who has aligned with rebel groups opposed to the deal, and Elhassan who has supported it.
Three DUP sources said Mirghani's return aimed to end the dispute in favour of Jaafer and against the deal, a move they said threatened to fracture the party further.
The DUP, which at its founding supported maintaining unity with Egypt following Sudan's independence in 1956, has close ties to Egyptian authorities.
The flight that Mirghani returned on was facilitated by Egyptian President Abdel Fattah al-Sisi, Egyptian state-backed AlQahera News reported. al-Sisi, a former army chief, also has close relations with Sudan's military leadership.