The ousted leader, 47, presented his "irrevocable resignation" on Sunday evening, the VMRO-DPMNE said in a statement.
Gruevski and several other conservative party members are under investigation over 2015 wiretapping allegations.
The scandal surfaced after Social Democrat Zoran Zaev released tapes that appeared to confirm official wiretapping of 20,000 Macedonians, including politicians and journalists, and high-level corruption.
The revelations led to Gruevski's resignation from government in January 2016 and plunged the country into a deep crisis.
The turmoil only eased when Zaev became prime minister in spring this year after striking a controversial deal with minority ethnic Albanian parties following snap elections in December.
Gruevski's successor is due to be elected at an extraordinary party congress on December 22 and 23.
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