I am about to install a sub panel. I purchased a 125 amp panel but the vendor only had a 100 amp breaker to feed my panel from the main panel. Would this be within tolerance?

Yes, what you plan is fine. The panel is rated 25 amps more than the breaker feeding it. No problem.

Generally, upstream circuit breaker or isolator shall be of higher rating than the down stream breaker. In your case if both the switches / isolating points are in near by area, there is no problem. (becasue of any fault in your panel; only 1 no. 100 ampere breaker is going to trip. You should put a warning sticker on your 125 ampere breaker that "to be loaded up to 80 ampere only") this is because you are receiving power from 100 ampere breaker.