The defeat ends the Toon's campaign in the UYL.
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Montrell Culbreath struck first for Bayer with a header before halftime.
Ferdinand Pohl then doubled Bayer's lead soon after the break as the hosts took control of the game.
Newcastle pulled one goal back through Kyle Fitzgerald late on, but it wasn't enough as the hosts held on for the win.
For the Toon, Isaac Moran, who joined the Magpies from Liverpool last summer, was handed his UYL debut. Thomas Bryant also was handed his first competitive start in 362 days after recovering from a long-term injury.
