How to use a transistor to pull a pin low?
Any hints on how to fix that?


A circuit would help instead of text diagrams but to answer your question, try putting the 10k resistor in the collector of the transistor not the emitter; emitter to ground like the reset pin circuit, base as per reset pin circuit.

You may be able to confirm my suspicions if you can tell what your base drive circuit looks like.

EDIT following disclosure of circuit

If you swapped the positions of R1 and SW1 in your second diagram, the pushbutton circuit would still operate as normal BUT, significantly for the BJT this is a different ball-park; the BJT will switch on and drag the 10k down to ground. 

Previously, when you tried the BJT in the original switch position you'd apply 3.3V to the base and approximately 2.7 volts would appear across the 10k resistor - this is because the base and emitter region act like a forward biased diode - even without collector current, the emitter voltage would be raised to 2.7V or thereabouts.