Not sure what you mean by 'opened up the rear brake fluid master cylinder'.....
If you loosened a fitting on the brake line, you likely got some air in the system. Time to bleed 'em.
If you just opened the reservior cap, that won't affect the braking power. Perhaps you got some grease or oil on the rotor?
In the future, you can gently pry between the pads to push the pistons back a little, that'll make it easier to get the caliper back onto the rotor. Then after reassembly, just pump the brake a couple times to push the pads back into position.
It only takes a little grease or oil contamination to feel a big reduction in braking power. Luckily, if it is only a little bit, sometimes it will cook out and /or carbonize from the heat of a few brake applications. I did that recently on the BMW front wheel - didn't remember getting anything on the disk, but after greasing the steering head bearings and changing fork oil it wouldn't stop for beans. A few laps around the neighborhood carefully and the grip came back.
I also buy brake parts cleaner in spray cans by the case at the local BJ's wholesale club (like Sam's Club). It's great for decontaminating brakes or just about anything.