Mastroeni struck first in the 35th minute and became the 13th different Colorado player to notch at least one goal this season. Nyassi then registered his fourth goal in the 45th minute after receiving a perfect through pass from Omar Cummings.
The defending MLS Cup champion Rapids (8-6-10) increased their unbeaten streak to three - 2-0-1.
Philadelphia's Roger Torres scored during stoppage time in the second half despite being a man down.
In the 64th minute, Union defender Sheanon Williams argued vehemently after a non-call and was eventually given a red card and ejected from the match. The Union played with 10 men the rest of the way.