Brandicourt had been widely tipped to become Sanofi's new boss, a position that opened when Chris Viehbacher was suddenly sacked last year.
The 59-year-old Frenchman, who researched tropical and infectious diseases before joining the corporate pharmaceutical world, will take over as CEO on April 2, Sanofi said.
"Olivier Brandicourt's strong experience combined with his international profile, deep knowledge of U.S. and emerging healthcare markets, and his capability to unite teams will provide new dynamism to Sanofi's strategy of diversification and innovation," Sanofi Chairman Serge Weinberg said in a statement.
Weinberg, caretaker CEO since Viehbacher's ouster, told shocked investors in October by saying that Viehbacher had been a poor communicator with the board and must take responsibility for faltering U.S. sales of key diabetes drug Lantus.
Weinberg said two weeks ago that a successor would be named by the end of March.
Sanofi is France's biggest listed company, employing 27,500 people in France, making up a third of the country's pharmaceuticals jobs and a quarter of the company's own worldwide workforce.
One of Viehbacher's mistakes was to develop a politically explosive plan to cut French jobs without telling the board.
Brandicourt, a 28-year industry veteran who also previously held an executive position at Pfizer Inc (PFE.N), spent his early adult life in France and should be attuned to national sensitivities.
"He has the necessary criteria to do this job," said Norbert Janisch, fund manager with Raiffeisen Capital Management in Vienna. "First of all, he is French and therefore well connected in France. And second, he knows the American market, which is important for a large pharmaceutical company."
Germany's Bayer had recruited Brandicourt only 17 months ago from Pfizer.
Bayer said that executive board member Werner Baumann will replace Brandicourt as healthcare division head, in addition to maintaining his responsibilities for group strategy, portfolio management and European markets.
This will likely bolster his position as front runner to replace Bayer CEO Marijn Dekkers, who last year said he would step down at the end of 2016.
Lantus, which accounts for over 30 percent of Sanofi's profits, is due to lose U.S. patent protection this year.
A replacement, Toujeo, is awaiting U.S. approval and is set for launch by June. It is arguably the most important of six Sanofi drug launches expected this year, including a potent new type of cholesterol fighter in partnership with U.S. biotech Regeneron Pharmaceuticals. (REGN.O).
Brandicourt is also seen as the right man to boost Sanofi's emerging markets portfolio, which represents a third of revenue.
After earning his medical degree, Brandicourt spent eight years with the Paris Institute of Infectious and Tropical Diseases focused on malaria research in West and Central Africa and worked as a doctor in the Democratic Republic of Congo.
Sanofi plans to launch a vaccine for dengue fever this year.
Brandicourt also has takeover credentials that may prove useful at a time when companies pressured by generic drug competition are becoming either predators or prey.
During Brandicort's brief Bayer tenure, the group bought Merck & Co Inc's (MRK.N) consumer care business for $14.2 billion and Norwegian cancer drug developer Algeta for $2.9 billion.
Reporting by Andrew Callus; Additional reporting by Noelle Menella in Paris, Ludwig Burger in Frankfurt, Carolyn Cohn in London and Bill Berkrot in New York; Editing by Alexandria Sage, Susan Thomas and Leslie Adler