Brandicourt had been widely critisised when he arrived at the company for pocketing a one-off welcome package of around 4 million euros (3.48 million pounds).
A presentation published on Sanofi's website stated Brandicourt was due to receive a fixed salary of 800,000 euros ($868,000) as well as a bonus of 1.16 million.
In a vote, more than 55% of shareholders rejected the proposed bonus.
Sanofi's chairman, Serge Weinberg, said in an online presentation the board would meet again to discuss the issue.
Brandicourt, a former executive with Germany's Bayer, joined Sanofi as CEO in 2015. He left the company at the end of August last year and was replaced by Paul Hudson, who joined from Switzerland's Novartis.
Under his tenure, Brandicourt reshaped Sanofi in a series of reorganisations and deals, including swapping the French group's animal health unit with the consumer healthcare operations of Germany's Boehringer Ingelheim in a $20 billion transaction.
Launches, such as eczema treatment Dupixent, cost-cutting measures and new priorities in research and development also helped the company return to profit, but Brandicourt and his teams failed to land two strategic acquisitions.
(Reporting by Matthias Blamont; editing by Barbara Lewis)
