Penilla ran onto a perfectly weighted ball from Juan Fernando Caicedo and slotted it past goalkeeper Luis Robles from a narrow angle.
Cody Cropper had five saves in his fourth start this year and the Revs (2-5-1) had their first clean sheet of the season. New England had lost five of its last six.
The Red Bulls (1-4-2) are winless in five games, losing four over that span.
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