The deal is likely to be revealed on 14 September in New York before the stock market opens.
Bayer's new offer is 2% more than its previous bid and about 19% more than Monsanto's last closing price.
Merger could create world's largest agricultural supplier.
CFO John Ramsay will take his place until a suitable replacement is found.
Countries remain sceptical of the safety of genetically modified crop varieties.
Monsanto said it will continue to focus on its growth opportunities built on its existing core business.
Syngenta earlier rejected a $45bn offer, saying it fundamentally undervalued its prospects.