Igathe wrote his resignation letter on January 12th but indicated that it would take effect on January 31st at 1pm.
Some Jubilee operatives had been leading talks to convince him to recall the resignation.
However on Wednesday and only ten minutes after the expiry of his notice of resignation, Igathe confirmed that he was leaving City Hall for good.
"It has been a great pleasure serving Nairobians & I will continue to serve as an advisor, beyond my previous position of Nairobi County Deputy Governor," Igathe tweeted.
He parted on a controversial and philosophical note, stating that Kenyans should change their ideology of fearing free thought "more than they fear electric shock".
It remains unclear if the statement was made in reference to his former boss Governor Mike Sonko, whom he blamed for his surprising decision to resign.
"Strength, progress & peaceful change comes from independent judgment & individual ideas. Compromise should be on issues, not of principles; on political positions, not ourselves. As Kenyans, we should aim to surpass the ideology that fears free thought more than electric shock," Igathe stated.