Despite routinely stranding runners on base - 16 in total - the Phillies eked out a stomach-turning 3-2 win, thanks to Lee and former Minnesota Twin Ben Revere.
"We had them all the way," manager Charlie Manuel said with a laugh afterward. "Are you kidding me?"
Despite banging out a season-best 16 hits, the Phils scored three runs last night.
It was just the second time in baseball history that a team had 16 or more hits and three or fewer runs and won in a nine-inning game. That team also happened to be the Phillies, in a 3-0 win over Pittsburgh on July 6, 1954.
Last night was also the 37th time in 66 games this season the Phillies scored fewer than four runs. The Phillies had lost 28 of those 36 games entering the night, including each of the previous four games on this road trip.
But pitching and timely offense, or at least when it was needed most, prevented the Phils from being swept in Minneapolis.
"That was a good team victory," Revere said.
While Lee was dominant through the first two-thirds of the game, Revere's bunt single keyed an eighth inning rally that sealed the Phils' first win in 7 days.
Revere, who had three hits on Wednesday, tied a career high with four hits last night.
"That's the best game I've seen him play," Manuel said of Revere, who is hitting .319 in his last 35 games. "That's the best game I've seen him play so far, without a doubt. That's the best I've seen him hit the ball, that's the best he's run - his speed definitely played a factor in the game tonight."
After pinch-hitter extraordinaire Kevin Frandsen, hitting for catcher Humberto Quintero, led off the eighth with a double, Revere attempted to bunt him over. But his speed allowed him to end up with a base hit, too.
Michael Young followed with a game-tying single to right and Jimmy Rollins brought home the go-ahead run on a groundout as the Phils rallied to avoid a potentially embarrassing defeat.
"Ben's bunt was something needed for us - something good," said Frandsen, who is 5-for-13 this month. "It was a good sac bunt and he beat it out. That was a big positive for us. I'm on third but now it's first and third, that changes the whole thing.
"We've waited too much for something to happen, and we created it right there. And it was good."
Although they cashed in two chips in the eighth, the Phillies had ample opportunities to score more. After Ryan Howard made the inning's first out with a strikeout, the Twins walked Domonic Brown intentionally to load the bases with one out. But Delmon Young grounded into an inning-ending doubleplay.
Through eight innings, the Phillies stranded a whopping 15 runners on base.
"I can't explain it," Manuel said. "But at least we got guys on base. We can always have a chance to knock them in is they're on base. Usually they're not on base."
But thanks to Lee - and the backend of the bullpen that was supposed to be a strength all season - three runs were enough.
Lee didn't allow a baserunner until Joe Mauer knocked a one-out single to left in the fourth inning. He didn't allow another until he walked Mauer in the seventh.
If it's June it must be time for Cliff Lee to hear trade rumors - something he has dealt with almost yearly for the last 5 years - and his dominance yesterday at the end of a forgettable week for his team brought the trade talk back up following the game.
"I know that I want to win and I'll voice that to whoever," said Lee, who acknowledged the Phillies have underachieved in the last two seasons. "And that's that. I want to win here. That's why I signed here. And that's where my focus is."
Last night, Lee's shutout bid - and the Phillies' lead, too - ended later in the seventh, when Justin Morneau laced a double just out of a diving Revere's reach in left-center. Two runs scored.
But after the Phils offense rallied to get both runs back in the next half inning, Mike Adams had a shot at redemption.
Adams, who took the loss two nights earlier, struck out the first batter he faced in a 1-2-3 eighth inning. It was just the third time in the last month Adams didn't allow a run. It was also Adams' first perfect inning since May 29. In that same game - 15 nights ago in Philly - Jonathan Papelbon had his most recent save opportunity before last night.
But Lee, Adams and an underachieving-yet-clutch offense handed Papelbon a one-run lead in the ninth and, like Adams before him, the closer was perfect to finish off an odd and long-awaited victory for Charlie Manuel and Co.
Whether or not the victory was a brief break from the nauseating defeats is the great unknown.
"The past year and a half hasn't gone the way I would have anticipated," Lee said. "It's why you play the games. You never know. I don't think anyone here is happy with the way we've played in that time frame . . . I can't look at it any other way, besides I expect us to win and catch up with the Braves and get into the postseason. That's the only way you can look at it."
Carlos Zambrano threw five innings last night at Triple A Lehigh Valley, allowing two runs on four hits to go with five strikeouts and four walks. The IronPigs defeated Scranton/Wilkes Barre, 4-2.
On Twitter: @ryanlawrence21