The agreement comes after Takeda revised its fourth proposal of £44.3bn, which followed the previous three offers of £41bn, £43bn and £44bn, respectively.
The combined group will be in a good position to deliver rare disease and plasma-derived therapies that will boost oncology drugs and vaccine development.
The group will build on current partnerships, including Takeda’s 180 active alliances with academia, biotechnology companies and startups, to bolster its existing pipeline.
Takeda president and CEO Christophe Weber said: “Shire’s highly complementary product portfolio and pipeline, as well as experienced employees, will accelerate our transformation for a stronger Takeda.
“Together, we will be a leader in providing targeted treatments in gastroenterology, neuroscience, oncology, rare diseases and plasma-derived therapies.”
Takeda expects that the respective geographic presence, scale and efficiencies, and research and development (R&D) capabilities of the companies will allow the combined entity to deliver more innovative medicines and transformative care.
Shire chairman Susan Kilsby said: “With this combination, Shire helps create an even stronger biopharmaceutical company, with a robust R&D pipeline and expanded global footprint.
“We firmly believe that this combination recognises the strong growth potential of our leading products and innovative pipeline and is in the best interests of our shareholders, our patients and the communities we serve.”
Subject to customary closing conditions and regulatory approvals, the acquisition is expected to be completed in the first half of 2019.
Upon completion, Shire will become a wholly-owned subsidiary of Takeda, which will own around 50% of the combined group.
The integration will be supported by the companies’ complementary organisational structures and manufacturing facilities in various geographic areas such as the US, Switzerland and Singapore.
The combined company will continue to have its headquarters Japan.