The dispute was triggered when Refaat slapped Emam last week, before the latter backed down on his complaint against the Zamalek icon.
However, Refaat was caught making an inappropriate comment about the 22-year-old midfielder and his wife on a live show on Dream TV when he thought he was off record.
The fresh setback forced Emam to seek legal action against Refaat, who was eventually sacked after just one month in charge.
The former Syria manager was relieved of his duties shortly before informing FilGoal.com of his willingness to resign.
"I intend to remove any discomfort within the club's board in the recent period," Refaat told FilGoal.com on Monday.
"I've been put under a lot of pressure recently because of the Emam crisis, which was mainly caused by Dream TV."
Refaat, a former manager of Zamalek, has been appointed in September as a new board, led by Galal Ibrahim, took charge of the Cairo club.
نرشح لكم
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Refaat sacked after inappropriate Emam remark
مياشر كأس العرب - المغرب (1)-(0) الإمارات.. أزارو يهدر الثاني