But it was Felix to rescue in the nightcap.
He took the series finale into the eighth inning before handing the ball to right-hander Brandon League, pressed into closer duty because David Aardsma was unavailable.
League got the five outs needed, enabling the Mariners to break even on a grueling four-city, 12-game road trip.
"It was a nice win to end our longest road trip of the year," interim manager Daren Brown said. "To end up 6-6 on the trip was big, especially going into two places, New York and Boston, that are tough places to play."
Not as tough, however, with Felix on the mound.
He beat the Yankees in New York and held the Red Sox to four hits and two runs (one earned) in a gut-it-out 122-pitch effort.
And in the sixth inning, he became the third-youngest pitcher since 1952 to reach the 1,000-strikeout mark.
The only pitchers younger than Hernandez, who is 24 years and 139 days old, to reach the milestone since '52 are Bert Blyleven (23 years, 121 days) and Dwight Gooden (23 years, 249 days).
The milestone victim was David Ortiz.
Hernandez joins Randy Johnson (2,162), Jamie Moyer (1,239) and Mark Langston (1,078) as Mariners pitchers in the 1,000-strikeout club.
"I am really happy about that," Felix said, "but I am [happier] to win the game."
Third baseman Jose Lopez, Hernandez's best friend on the team, drove in two runs for the Mariners, who stranded 12 runners.
Felix went into the game working on a streak of 22 2/3 consecutive innings without allowing an earned run. He extended it five more innings before J.D. Drew hit a solo home run with one out in the sixth inning.
The streak appeared to have ended in the third inning, when Ryan Kalish, who reached on a one-out double and advanced to third on the first of two errors in the inning by shortstop Josh Wilson, scored on a wild pitch.
After the inning, the official scorer ruled that it was an earned run. But it was then pointed out that Wilson was going to throw Kalish out at third base and therefore should have been ruled an unearned run.
The scorer agreed and changed the ruling.
A game-within-a-game moment occurred in the second inning, when Felix faced former Mariners teammate Adrian Beltre for the first time in their careers.
Hernandez won, zipping a called third strike past Beltre for the second out of the inning.
It would be their only meeting of the game.
After Hernandez fanned Daniel Nava to end the inning, Beltre grabbed his glove and went to his position at third base. He wasn't happy.
The usually mild-mannered Beltre said something to plate umpire Dan Bellino and was ejected for only the second time in his career. The first one happened in 2002 with the Dodgers.
Before play resumed, Red Sox manager Terry Francona also was tossed.
The Mariners watched the ruckus from a distance, and then went about extending the one-run lead they gave Felix in the first inning.
Wilson started the third inning with a double to left field and advanced to third on Ichiro Suzuki's infield single. Ichiro stole second and both runners scored on Lopez's second hit, a single up the middle, putting the Mariners ahead by three runs.
The Mariners scored their fourth run off starter Tim Wakefield in the sixth on doubles by Casey Kotchman and Matt Tuiasosopo.
"I thought Felix was outstanding again," Brown said. "That one inning, when we made a couple of fielding miscues, cost him some pitches and ultimately caused him to come out in the eighth.
"Otherwise, he wasn't in a lot of trouble other than that inning."
It wasn't apparent until the eighth inning that Aardsma was not available. The Mariners had a two-run lead and he was not throwing.
The ball that hit him on the right side when he notched a save against the Orioles on Aug. 18 -- the last time he pitched -- remains a little tender.
"He has thrown a couple of times and we expect him to be ready to go on Friday," Brown said. "He's really close, but it's something we are being really careful with."
League notched his fourth save, retiring Ortiz on a hard line drive to Tuiasosopo in left with the potential tying run on base.
Hernandez, meanwhile, improved to 10-10 and lowered his ERA to 2.47 -- second in the American League.
"He not only has the stuff, but he's an outstanding competitor," Brown said. "He wants to win, he wants to face hitters. I really think that when guys get on base, he turns it up a notch.
"You know when he takes the mound, something special can happen that night."