Edit: The high impedance is only for the voltage measurement setting. The impedance is much much lower when measuring capacitance.
According to Fluke:
A multimeter determines capacitance by charging a capacitor with a known current, measuring the resulting voltage, then calculating the capacitance.
They are not waiting for the RC time constant. It applies a known current for a certain time and looks at the ΔV. They may also do the same thing discharging the cap, in a loop.
Higher ΔV means lower capacitance.