New England (5-3-2) extended its unbeaten run to five matches (4-0-1), and snapped a four-match winless slide against Seattle.
The Sounders (7-3-1) had their six-match (5-0-1) unbeaten run ended and the MLS' No. 1 ranked offense was shut out for the first time this season.
Fagundez scored his first two goals of the season in the 29th and 41st minutes for the Revolution.
Rookie Patrick Mullins, making just his third appearance, scored his second goal in as many matches to put New England ahead in the 14th minute.
Teal Bunbury banged in a rebound of his own shot off the left wing in the 36th minute for New England's third goal. And his drive off the right wing in the 46th minute was deflected off Seattle defender Chad Marshall for an own goal the Revolution's fifth of the match.
New England scored four goals during a first half for the eighth time in club history. Mullins converted a loose ball for the Revolution's go-ahead goal. Fagundez finished off a pass from Chris Tierney atop the penalty box area with a one-timer of a right-footed shot short side past Seattle goalie Stefan Frei, then took a long ball from Bunbury off his chest and polished off another right-footed shot to the far right corner of the Sounders net.
New England goalie Bobby Shuttleworth, who has allowed just two goals during the five-match unbeaten run, posted his fourth shutout. Seattle's best chances occurred on a header by Marshall in the 54th minute, a drive by Gonzalo Pineda in the 76th minute and another from the left by Kenny Cooper in the 77th minute.
The Sounders now return home to face San Jose next Saturday. Start time is scheduled for 7pm at CenturyLink Field.