Plans for the concrete tower topped by glazed viewing platforms, gondola ride attraction and educational facilities called sky classrooms had originally been approved by the government agency before the mayor used his right to veto.
Khan rejected the design because it was not a piece of "world class architecture that would be required to justify its prominence" and would give "very limited public benefit" to London.
British architect Norman Foster has defended his practice's design for the Tulip, saying the tower will become a "symbol in it's own right" on the London skyline.
"Like the Gherkin nearly twenty years ago, it is inevitably controversial, like the Gherkin it has the possibility of being a symbol beyond its host city," said Foster.
The project is funded by billionaire Jacob J Safra, who bought the Foster + Partners-designed Gherkin in 2014. Officially called 30 St Mary Axe, the office building won the Royal Institute of British Architect's Stirling Prize in 2004.
The Tulip would be built on a piece of land next to the 180-metre-high Gherkin, towering over it.
Controversy has surrounded The Tulip since the first visuals of the project were released in November 2018.
London City Airport voiced concerns that the tower could disrupt its radars, but an assessment undertaken by NATS (formally National Air Traffic Services) concluded the tower and its gondolas wouldn't have an impact.
The Greater London Authority (GLA) published a report January 2019 stating that The Tulip was in breach of its guidelines for London, because the viewing elements of the project would not be freely accessible to the public.
The Tulip was originally set to open in 2025. If built, it would be the tallest structure in the City of London.
Images by DBOX.