The generic drugmaker listed $10 billion of debt and $10 billion of assets.
The deal expands Gilead's investment in the European biotech as it seeks to add assets to its drug portfolio.
The privately held cancer drugmaker had been set for a public offering Wednesday.
Sales from Pfizer's innovative health division were particularly strong in the second quarter, with anti-smoking drug Chantix up 8% to $8.2 billion.
The deal is the largest-ever by a Japanese company and gives Takeda a lucrative portfolio of rare disease drugs.
The deal gives the Swiss drugmaker a neurological disease treatment that may have "a multi-billion dollar peak sales potential."
The drugmaker says "there is no alternative" to its restructuring plan amid pricing pressure on its core generics business.
Smiley takes over from Derica Rice amid a cost-cutting push aimed at freeing up cash for Lilly to invest in developing new drugs.
The drugmaker is restructuring as it tries to rebuild its drug pipeline amid investigations of its sales practices.
The drugmaker is seeking to become "a leaner, more nimble global organization" as it invests in a new generation of medicines.
