Sagan sit top of the J-League after 18 rounds with 37 points, ahead of second-placed Urawa Reds on goals scored.
But their success so far this season was not enough to save Yoon, with technical director Takayuki Nagai claiming the South Korean coach did not do enough to keep his fringe players happy.
"Attention and care (toward players)," said Nagai, when asked what the problem with Yoon was.
"There's no problem with those who are playing, but there are those who aren't playing. It's his way of leading [those who aren't playing that concerns the club]."
Nagai confirmed that assistant coach Megumu Yoshida will take over from Yoon.
"It was a painful decision. We are in first place but if we fall apart at the seams when something happens, we wonder if we can maintain our position in first," Nagai said.
Yoon led Sagan into Japan's top tier of football for the first time in 2012, after they finished second in J2 in 2011, and the 41-year-old had steered them to 12 victories, a draw and five defeats so far in 2014.
Sagan have never won the J-League.
Yoon is the fourth J-League coach to lose his job this season - all four are not from Japan.
Australia's Graham Arnold survived just eight games with Vegalta Sendai having failed to register a win, while in June, Cerezo Osaka and Shimizu S-Pulse respectively sacked Serbian Ranko Popovic and Iranian Afshin Ghotbi.
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