After the Revolution defense was humiliated in consecutive defeats, coach Brad Friedel was fired Thursday and replaced by interim coach Mike Lapper, who had his team properly motivated.
The Revs gave up 11 goals in the previous two games, but held the Earthquakes scoreless until the 88th minute when Valeri Qazaishvili scored his first of the season. New England goalkeeper Matt Turner made six saves in his second start of the season.
While New England (3-8-2, 11 points) won for the first time since April 20, San Jose (3-6-2, 11 points) saw its four-game unbeaten streak end. The Revs had gone 0-3-1 since a 1-0 victory over the New York Red Bulls last month, outscored 18-5 in those four games.
New England moved on from the disappointing Friedel era quickly as Agudelo poked a right-footed shot past Quakes keeper Daniel Vega in the 18th minute. Edgar Castillo sent in a left-footed centering pass and Agudelo redirected it into the goal for his second of the season.
Just 11 minutes later, Teal Bunbury was fouled by San Jose defender Harold Cummings in the penalty area. Cummings was called for a foul with his left hand to Bunbury's shoulder.
After video review confirmed the foul, Penilla delivered a successful penalty kick past Vega, giving New England its second successful PK this season in four tries. Gil added a second-half insurance goal in the 68th minute, his fourth.
It was the most goals scored in a victory for the Revolution this season.
San Jose forward Chris Wondolowski appeared in his 300th career MLS game when he came on a substitute in the 60th minute. The former U.S. Men's National Team member, who has World Cup experience, is just the fifth player to play in 300 MLS games with one club.
Revolution start post-Friedel era with dominant win
New England pummeled San Jose in their first game since former head coach Brad Friedel was fired, beating the Earthquakes 3-1 at Gillette Stadium.
Agudelo puts Revs ahead in first game after Friedel firing
Major League Soccer: Juan Agudelo (18') New England Revolution 1-0 San Jose Earthquakes