"I have no option but to resign from the office of premier," she said on Friday.
She will also leave parliament as soon as a by-election for her seat can be held.
Ms Berejiklian did not take questions from journalists after saving she had always exercised her duties with "the highest levels of integrity".
She will remain premier until her successor is anointed. She ascended to the NSW top job in early 2017.
The Independent Commission Against Corruption said in a statement on Friday that it was investigating whether Ms Berejiklian "exercised public functions" in a position of conflict between her public duties and private relationship with Mr Maguire, revealed in late 2020.
A public inquiry on the matter will be held from October 18, overseen by ICAC Assistant Commissioner Ruth McColl SC.
It is expected to last about 10 days.
ICAC said Ms Berejiklian would be investigated over grant funding to the Australian Clay Target Association in 2016/17 and grant funding to the Riverina Conservatorium of Music in Wagga Wagga in 2018.
It plans to look into whether Ms Berejiklian's relationship with Mr Maguire, then the Wagga Wagga MP, affected those arrangements and constituted a breach of public trust or partial exercise of official functions.
ICAC will also investigate whether Ms Berejiklian should have "suspected on reasonable grounds" that Mr Maguire may have engaged in corrupt conduct, and thus failed to report him to ICAC as required.
It will look into whether she "was liable to allow or encourage" his conduct.
Mr Maguire is accused of abusing his public office while serving between 2012 and 2018 as a state MP.
He's accused of using his public office and parliamentary resources to improperly gain a benefit for himself or for G8way International, a company Mr Maguire allegedly "effectively controlled".
Mr Maguire was forced to quit Ms Berejiklian's government in 2018 after a separate ICAC inquiry heard evidence he sought payments to help broker deals for property developers.
The pair's five-year relationship was kept secret until Ms Berejiklian disclosed it at an ICAC hearing in October 2020.
AAP with The Project
