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I am trying to trigger input pins on a controller (which I am not able to modify) with the raspberry pi. I know that the other controller's input pins are pull up, so I need to pull them down to trigger them. Will the raspberry pi pull down the controller pins?

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Yes.

The Raspberry Pi GPIO will pull an external pin down to ground.

For instance the Pi has hard wired 1.8kΩ pull-ups to 3V3 fitted to GPIO 2 and 3 (pins 3 and 5) and can pull them down to ground when GPIO 2 and 3 are set as a low output.

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