Bayer said that 2,850 administrative jobs will go, while 1,400 research and development positions are to be cut along with 1,850 production jobs.
Leverkusen-based Bayer said that savings from the deal would total $925.75m from 2009.
Werner Wenning, Bayer's chief executive, said in a statement: "We want to create an internationally successful pharmaceutical company with competitive cost structures.
"We said right from the start of the integration that job cuts would be necessary in order to achieve the synergy targets."
The merged company, called Bayer Schering Pharma and based in Berlin, has already begun talks with unions about the decision, but did not say if there would be buy-outs.