Ali, 35, the son of Jordan's late King Hussein and Queen Alia, will become the youngest member of the ExCo after beating South Korean Chung, who has sat on the board since 1994, by 25 votes to 20 in a fight for Asia's vice-presidential seat on the committee.
Prince Ali, who has been head of the Jordanian FA since he was 25, becomes the third member of the Jordanian Royal family to occupy a seat on a major sporting governing body.
His elder brother Faisal and sister Haya are both members of the International Olympic Committee while Haya is also president of the International Equestrian Federation.
Before the vote was taken Prince Ali told Reuters: "I am optimistic, but in a secret ballot you never know. However, I think I can bring some new ideas to FIFA, it is an exciting time for Asian football and I am standing because I think it is time for a change."
The ensuing result strengthens FIFA president Sepp Blatter's grip on his position as he privately supported the prince against Chung, one of his perennial critics.
Blatter is standing for re-election for a fourth term as FIFA president later this year.
Blatter told reporters afterwards: "This is a surprise. After 16 years, probably the youth that wanted to come in has played the better card. However, I did not support anybody."
Chung has long been one of the most influential FIFA executive committee members and in the late 1990s was one of the architects of South Korea's bid to stage the World Cup in 2002.
With the tournament seemingly destined for Japan, Chung manoeuvred then-president Joao Havelange, who supported Japan, into a compromise and for the first and only time, the World Cup was shared between two host nations.
It represented a major success for the Korean, whose family own the giant Korean Hyundai conglomerate.
Chung has been tipped as a possible future FIFA president, and although he has been voted off the executive and that is now unlikely to happen, he could still pursue the presidency, which is not restricted to executive committee members.
Blatter himself was FIFA's secretary general before he beat UEFA president Lennart Johansson to become president in 1998.
SEPARATE VOTE
In a separate vote between four candidates for two of Asia's other seats on the committee, Worawi Makudi of Thailand retained his seat and Vernon Manilal Fernando of Sri Lanka was voted on to the FIFA executive committee to replace Junji Ogura of Japan who was retiring.
Makudi polled 24 votes, Fernando 23. Kohzo Tashima of Japan and Zhang Jilong of China were the unsuccessful candidates.
Earlier, Mohamed Bin Hammam was re-elected as president of the AFC for a third and final term by acclamation of the Congress.
The 61-year-old Qatari, whose country will host the World Cup finals in 2022, was the only candidate for the position.
Sheikh Ahmad Al Fahad Al Sabah, the head of the Kuwait Football Federation and the Olympic Council of Asia, wh
