After hitting a two-run blast in the seventh, Burnitz went back-to-back with Phillips in the ninth. Burnitz has 18 career multi-homer games.
Vaughn's fourth-inning homer, his first in 11 days, came off starter Tomo Ohka (13-8) and gave the Mets a 3-0 lead.
Jason Middlebrook (2-3) -- the ninth starting pitcher used by the Mets this season -- gave up two runs and three hits in five innings. The righthander struck out five and walked two in his first start since being acquired from San Diego on July 31 along with reliever Steve Reed for lefthander Bobby Jones and two minor leaguers.