Fernandes was a last-minute replacement for Union captain and midfielder Brian Carroll, who was scratched just before the game because of an illness.
The Union were coming off a 1-1 draw at Portland in their opener. Philadelphia improved to 4-0-2 against New England at PPL Park.
The Revolution were shut out for the second straight game. They began the season with a 4-0 loss at Houston and will play four of their first five games on the road.
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