The Senegalese former diplomat is to begin her new role as of August 1 for a period of six months to be renewed if both entities agree, reports Efe news.
"Samoura will be assisted by a group of experts who will work in a spirit of partnership with President Ahmad and his team in several areas," FIFA said in a statement on Thursday.
Samoura is to "oversee operational management of CAF, including governance and administrative procedures, ensure the efficient and professional organisation of all CAF competitions" among other tasks she has been appointed to carry out, it added.
Following the announcement, which came a day before the kick off of the 2019 African Cup of Nations, Ahmad said that he asked for FIFA's help to "ensure that CAF functions with transparency, efficiency while abiding to the highest governance standards".
The CAF President told Efe that he had sought FIFA's guidance to assess the situation, two weeks after he was arrested and interrogated in France for an alleged corruption case.
"It is not FIFA that takes control under CAF, but CAF needs FIFA because you (press) never agree," Ahmad said.
"There is no corruption and you continued to talk about I am corrupted," he added in reference to information published by the press about corruption accusations.
"But what can I do? I called FIFA to help me. To clarify this situation."
According to a joint statement, the CAF executive committee unanimously approved its president's proposal.
Samoura is set to remain the FIFA general secretary, although she will delegate some of her tasks within the international governing body.
This was the first consequence after the French Prosecutor's Office arrested and interrogated Ahmad for a period of 24 hours on June 5, after he attended the FIFA Congress in Paris.
French authorities are still investigating allegations of corruption, breach of trust and falsification with regards to the contract signed in December 2017 between CAF and Puma sports brand about the supply of equipment for the previous edition of the Africa Cup of Nations, which was not fulfilled by the African body.
Following the arrest of Ahmad, FIFA issued a statement claiming it has no information about the reasons for his arrest and added that it is committed to fighting against corruption.
"FIFA is now clean from the scandals that tarnished its reputation and this same determination should prevail in governing bodies such as confederations," a statement released at the time said.
In April, CAF Secretary General Amr Fahmy was fired after denouncing alleged bribes and the diversion of hundreds of thousands of dollars.
( With inputs from IANS )