Pepi first beat Revolution goalkeeper Matt Turner in the 11th minute, running onto a quick through ball from fellow homegrown Jesus Ferreira following a turnover in midfield.
Pepi then found his second in the 54th minute, beating Revolution center back Jon Bell after Ryan Hollingshead played a harmless pass up the left sideline.
In between Pepi’s right-footed finishes, New England drew level at 1-1 in the 33rd minute through Gustavo Bou.
New England made several attack-minded substitutions while pushing for an equalizer, but couldn’t seriously threaten FCD goalkeeper Jimmy Maurer.