The series of changes, announced on Sunday, include state in-charges, convenors and people in charge of the party's various fronts.
Mr Shah, who has several criminal cases against him and is out on bail, had received a big promotion in the party in March this year, and was appointed as a General Secretary. The elevation was a sign of the growing influence that Mr Modi now wields in the BJP.
But the party categorically denounced the Modi factor in the latest appointment. "Narendra Modi has recommended nobody... he (Shah) has been a successful minister in Gujarat... I am sure he will be useful in UP," said party chief Rajnath Singh.
Meanwhile, Mr Gandhi, fresh from an all-clear from courts in hate speech cases, has been given responsibility of a state headed by the Mamata Banerjee-led Trinamool Congress.
In other important assignments, the BJP appointed Andhra Pradesh strongman Bandaru Dattatray as one of its Vice Presidents. He has also been made the party in-charge of Kerala. He replaces Sadananda Gowda as party Vice President, who resigned after becoming Leader of Opposition in Karnataka Legislative Council. Mr Dattatray was a minister in the Atal Bihari Vajpayee government.
Rajiv Pratap Rudy, who was recently elevated as General Secretary, has been appointed in-charge of Maharashtra, another crucial state where Congress and NCP have been in power for the past several years.