Boston rallied with three runs to take a 6-5 edge against starter Tim Redding (0-1) in the fifth. George Kottaras' RBI double chased Redding before Green singled home two runs on the first pitch from reliever Sean Green.
Jason Bay had an RBI single before Drew added a run-scoring double in the sixth. Youkilis homered against Brian Stokes, capping a four-run seventh.
The video-replay system at Fenway Park got used for the second straight day, and umpires upheld their call that Youkilis' drive toward the left-field pole was foul.
On Saturday night, Santos' long fly that hit off a table in the first row of the Green Monster seats and bounced back onto the field - initially ruled a double - ended up being called a homer when the umpires used the first replay review in the park's history.
Tim Wakefield (6-2), the club's most consistent starter so far this season, gave up five runs and seven hits in six innings for his fourth win in five starts. It was the seventh time in nine starts that he's pitched at least six innings.
David Ortiz went 0 for 5 and stranded eight runners, dropping his average to .195.
Trailing 3-1, the Mets scored three in the third. David Wright and Jeremy Reed had consecutive RBI singles after Carlos Beltran's run-scoring ground out.
Gary Sheffield's RBI single made it 5-3 in the fifth.
Jacoby Ellsbury extended his career-high hitting streak to 19 games.
Lowell's three-run homer gave Boston a 3-1 lead in the second after Ramon Castro homered off the left-field pole foul for the Mets.
Ortiz, who changed to a lighter colored bat from usual black one his third time up, ended the second and fourth with two runners on each time.
Redding, signed as a free agent in January, made just his second start after opening the season on the disabled list with a strained rotator cuff.
A thunderstorm in the bottom of the first inning forced a 36-minute delay.
Notes: Mets manager Jerry Manuel expects SS Jose Reyes, sidelined since Wednesday with tendinitis behind his right calf, to play Monday when they host Washington. He also said OF Beltran, who was the DH this weekend because of a bruised right knee, could play Monday if he feels the same. But OF Ryan Church, who left Friday night's game with a sore right hamstring, was still unavailable...Red Sox manager Terry Francona played SS Green for the second straight game after saying before Saturday's contest that Julio Lugo would play one and Green the other. Boston improved to 18-6 when Green starts.
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