Umno president Datuk Seri Najib Tun Razak also reappointed Tengku Adnan as secretary-general while Finance Minister II Datuk Ahmad Husni Hanadzlah as party treasurer.
Najib loyalist and deputy Pontian Umno chief Ahmad Maslan cemented his position as a rising star in the party when he was appointed information chief.
Ali remains Malacca Umno chief while party vice-president Datuk Seri Hishamuddin Hussein as Terengganu Umno chief.
Asked about the appointment of old faces into the council such as Rafidah, Najib said: "They can still contribute to the party."
Rafidah lost her Wanita chief post to Datuk Shahrizat Jalil in the recent party polls.
The Malaysian Insider understands Ali was appointed because of his popularity in the party. He had been a front runner to win the deputy party presidency until he was found guilty of being involved in vote-buying.
By appointing Rafidah and Ali, two of the most significant losers in the recent party polls, Najib could draw flak from the public in his push to put forward a clean party and government leadership team.
Najib also announced a reshuffle of state party leaders which saw the three vice presidents leading the party in "problematic" states.
Datuk Seri Hisammuddin Hussein takes over the post of Terengganu Umno chief from Menteri Besar Datuk Ahmad Said who has lost the support of Barisan Nasional lawmakers in the state.
"The matter of mentri besar is a separate issue," said Najib.
In Perlis however the state party will be led by Menteri Besar Datuk Md Isa Sabu, who replaces local strongman and former MB Datuk Seri Shahidan Kassim.
In Penang, Datuk Seri Ahmad Zahid Hamidi replaces Tun Abdullah Badawi, the former prime minister, as state party chief.
Another vice president, Datuk Seri Shafie Apdal, is now the Kedah Umno chief replacing former Menteri Besar Datuk Mahadzir Khalid.
Najib himself will lead the party in Selangor replacing defeated Umno deputy presidential contender Tan Sri Muhammad Muhd Taib.
Newly elected deputy president Tan Sri Muhyiddin Yassin was appointed Federal Territory Umno chief.
For Perak, Menteri Besar Datuk Seri Dr Mohd Zambry Kadir takes over the state party leadership.
In Negeri Sembilan, Malacca, Johor and Sabah, the respective mentris besar or chief minister were retained as the state party chief.
Others appointed to the supreme council were Datuk Kamilia Ibrahim, Datuk Razali Ibrahim and Dr Wan Norashikin representing the three wings, Wanita, Youth and Puteri respectively.
Also appointed were Datuk Seri Nazri Aziz, Datuk Jamil Khir, Raja Nong Chik, Datuk Aziz Sheikh Fadzir, Datuk Abdul Ghani Othman and Datuk Seri Shahidan Kassim.