The move means Dr Daniel Manduku can now take over as MD.
The petitioner said the application had been overtaken by events.
However, he said the petition challenging the process to send the former MD on leave remains.
The High Court has lifted orders it had issued suspending a decision to send former Kenya Ports Authority (KPA) managing director Catherine Mturi-Wairi on compulsory leave.
Justice Eric Ogola set aside the orders following the withdrawal of the application by the petitioner.
The order had also stopped the subsequent appointment of Dr Daniel Manduku to the position, meaning the former National Construction Authority (NCA) boss can now take over as MD.
The petitioner's lawyer, Gunga Mwinga, told the court Tuesday that following the resignation of Ms Mturi-Wairi, the application had been overtaken by events. However, he said the petition challenging the process to send the former MD on leave remains.
The application had been filed by a Kilifi resident, Emmanuel Chengo Kenga, who had argued that the KPA board's decision to send her home was unconstitutional.
Ms Wairi penned a resignation letter to Transport CS James Macharia last Friday, marking the end of her 25-year career at the State body.
Two separate suits had been filed - at the Mombasa High Court and at the Employment and Labour Relations Court - challenging her ouster.
The latter, filed by activist Okiya Omtata, also sought to prohibit the KPA board and the Attorney General from replacing her with Dr Manduku in an acting capacity.
Justice James Rika will deliver a ruling on Thursday on whether to grant the conservatory orders sought by Mr Omtata.
Last Wednesday, the government appointed retired General Joseph Kibwana as the new KPA board chairman, replacing Major (Rtd) Marsden Madoka whose term ended.
