The German drugmaker had received all required approvals from regulatory authorities, it said in a statement on Monday.
"Bayer will remain the company name. Monsanto will no longer be a company name. The acquired products will retain their brand names and become part of the Bayer portfolio," it said.
Bayer launched a 6 billion euro ($7 billion) rights issue on Sunday, a cornerstone of the financing package for the deal, shortly after clearing the last major antitrust hurdle in the United States.
The deal is the first of a trio of major U.S.-German merger deals to cross the finish line at a time of harsh criticism by U.S. President Donald Trump of Germany's trade surplus with the United States.
Deutsche Telekom's T-Mobile US plans to merge with Sprint for $26 billion, while industrial gases makers Linde and Praxair are also seeking to combine.
Bayer was expected to rid itself of the target's name. Monsanto, the largest - though not the only - maker of genetically modified seeds, has been a lightning rod for environmentalists' opposition to the technology.
The U.S. seed-maker has also drawn criticism for pursuing its intellectual property rights with farmers, many of which depend on its seeds, more aggressively than its peers.
"We aim to deepen our dialogue with society. We will listen to our critics and work together where we find common ground. Agriculture is too important to allow ideological differences to bring progress to a standstill," Bayer Chief Executive Werner Baumann said in the statement.
The companies' separately listed Indian units, Bayer CropScience and Monsanto India, will continue to operate independently, for the time being, Bayer said in a separate statement.