Hong Kong born Chan, a veteran of more than 80 films including First Strike and Rush Hour, topped the survey last year with 17%.
In a poll of popular screen stars, conducted by a marketing company in Hong Kong, Yun-Fat grabbed the most public support with 18% of the votes.
However action hero Chan, 45, who took the lead in the same poll last year, was pushed into second position after securing only a 7% share.
Hong Kong born Chan, a veteran of more than 80 films including First Strike and Rush Hour, topped the survey last year with 17%.
He is thought to have been sidelined this time - despite his long-standing popularity with film audiences - because he recently confessed to having fathered an illegitimate child.
He admitted to having been unfaithful to his wife with former Miss Asia, Elaine Ng - who later bore him a daughter.
Fall from grace
"The drop in Jackie Chan's ranking may or may not be related to his recent scandal," said Anthony Lau, chairman of the Hong Kong Advertisers' Association which sponsored the survey.
"It shows the risk of a celebrity's endorsement. Their popularity can change unexpectedly," he told the South China Morning Post.
Chow Yun-Fat, 44, was also born in Hong Kong and has appeared in more than 70 films. But, it is his role as the 19th century King of Siam that has thrown him into the limelight.
He stars alongside acclaimed actress Jodie Foster in the epic Anna and the King, which was nominated for an Oscar at this year's Academy Awards.
However, the movie has also stirred up controversy. A remake of the 1946 feature starring Rex Harrison and Irene Dunne, it tells the story of an English governess in the court of King Rama IV.
But censors in Thailand have banned the film after branding it an insult to the monarchy and a distortion of Thai history.