To rebuke
means to command something or someone to stop doing something. When the Lord rebukes, the command is effectual. That which God rebukes stops doing what it was doing. For example, God rebuked the Egyptian army (Psalm 76:6), and they lay still. They stopped pursuing the Israelites. In Isaiah 50:2 the Lord rebukes the sea and it dries up. He rebukes the rivers and they stop flowing. In Malachi 3:11 the Lord rebukes the devourer (such as locusts), and they stop devouring.
In this verse, the Lord rebukes the offspring of the Levites. This means that they stop serving as priests. God puts an end to their priestly service.
3 Behold, I will rebuke your offspring, and spread dung on your faces, the dung of your offerings, and you shall be taken away with it.