A sumptuous strike from the Stoke-bound forward separated the two Eastern Conference teams.
Agudelo's goal was a fine piece of invention a few minutes after the restart. Running onto a long ball from Chris Tierney, the forward let it bounce once before hitting the second bounce with the outside of his heel behind his back.
The ball then went up and over Sean Johnson and into the net despite Bakary Soumare's desperate attempt to intervene on the line.
New England leapfrogs Chicago into sixth place now, with 33 points to the Fire's 31, although Chicago has a game in hand.