Boston's Manny Ramirez made it a league-most 42 home runs allowed by the Twins, who just shrugged off the early deficit and went back to playing the way they always have.
Hernandez won again, Craig Monroe contributed another big hit, and the Twins beat the Red Sox 7-3 to win the four-game series and improve to 14-7 at home.
"There may be new characters in the clubhouse, but it's the same philosophy," said Michael Cuddyer, who had two hits and knocked one in.
Ramirez hit career homer No. 498 in that first inning, a two-run shot that gave him only his second home run in 20 games and gave the Red Sox a 3-0 lead.
But Hernandez (6-1) rebounded after that rough start to finish six innings for another quality outing, and the Twins are now 8-1 when he's on the mound.
"Maybe they don't got the power like the other teams, but it's a good-hitting team," Hernandez said. "You've got to concentrate on something to try to stay long in the game. I kept thinking all the time that three runs is not going to make a difference."
Red Sox starter Clay Buchholz (2-3) didn't make it out of the fifth, done in by control problems and timely hits by the Twins -- who took three games and reduced the Red Sox lead in the AL East to a half-game over Tampa Bay. That's their smallest since May 1.
"It's tough, but you have to give the Twins credit," Ramirez said. "They have a great bullpen that pitched great, and you have to tip your hat to them."
Juan Rincon pitched two hitless innings, and Jesse Crain got Ramirez to fly out to center field to end a scoreless ninth. Minnesota has won nine of its last 12 games and scored 74 runs in the process.
"Everybody's starting to swing the bats, and it'll be fun around here when we start to see everyone get going," said Monroe, who hit a two-run double in the decisive three-run fifth.
The Twins have done it almost entirely with singles, speed and smart baserunning. Their 20 homers rank one ahead of Kansas City for the fewest in the majors, and they beat up Buchholz for seven runs in 4 1/3 innings with only one extra-base hit.
Monroe, who hit two homers in Sunday's 9-8 win, has so far been a pleasantly productive part-time DH for the Twins. Monroe, acquired from the Cubs for minor league outfielder Doug Deeds, is batting .290.
Hernandez, another unheralded acquisition during a hectic winter, has been a huge help for the first-place Twins. Minnesota has won all three of his starts this month by a combined 31-5 score, and he has allowed only five runs in 22 innings.
"He changed his speed a lot, with good location," Ramirez said. "When he's on, he's on, and he pitched great. You have to give him credit."
Over his last two starts, Buchholz has surrendered 18 hits and 12 runs in just 8 1/3 innings. He walked five this time, twice putting Mauer on to lead off an inning and watching him come all the way around.
"I don't know what anybody can tell me," Buchholz said. "It's sort of in my hands right now. I was leaving pitches up, and they got hit. That's what happens."
Just about everything fell Minnesota's way in this series, good vibes no more evident than in the top of the seventh inning when Dustin Pedroia hit a routine line drive to right field straight at Cuddyer.
He casually reached for it, when the ball popped out of his glove, bounced on the top of his cap, off the brim and back into the mitt. Cuddyer mouthed a "wow" and flashed a sheepish smile.
"It was definitely not a trick," said Cuddyer, an accomplished magician.
The Twins will take their time with RH Scott Baker, who was placed on the DL last week due to a problematic right groin strain and essentially replaced in the rotation by LH Glen Perkins. Manager Ron Gardenhire said Baker won't be allowed to throw full speed off a mound for at least another 10 to 12 days. ... The Red Sox released LH Abe Alvarez to make room on Triple-A Pawtucket's roster for IF Jed Lowrie, who was sent down Sunday. Alvarez was a second-round draft pick in 2003 who made brief appearances with Boston in 2004, 2005 and 2006, but was sidetracked the last two seasons by ankle and oblique injuries. ... Twins LF Delmon Young twisted his left ankle in the eighth inning, but was determined to stay in the game. He has played in 202 consecutive games, but Gardenhire said he should be fine to play Tuesday pending evaluation. "It's up to me when I come back," Young said. "It's my body, so if I can play on it then I can play." ... J.D. Drew had his third three-hit game of the season for Boston and raised his average to .301.