Philadelphia collected 14 hits off starter Kerry Wood and five relievers, including six in a nine-run sixth inning, when Wood faced seven batters and failed to retire any of them.
So now the Cubs go to Minute Maid Park for a weekend series against the first-place Astros, who are 32-18 at home.
Until Bobby Abreu's grand slam erased a 3-1 lead and sparked the Phillies' nine-run sixth, it seemed the Cubs might achieve Baker's pregame hope.
"We can split the series today and stay above. 500," he had said. "Hopefully we can pick up a game and go into Houston with some momentum. We don't want to go into that lions' den on a downer. Those guys play exceptionally well at home."
Baker also expressed hope Wood, seeking his third straight complete game, could pitch deep into the game to keep the bullpen rested.
"A couple of early exits in a row put pressure on our bullpen," Baker said. "Thank God for [Wood]."
Wood held the Phillies to a run and two hits and struck out nine in the first five innings, but he unraveled in the sixth after failing to make the play on Marlon Byrd's leadoff bunt right back to him.
It went for a single when Wood failed to field it cleanly.
In short order Placido Polanco singled to right, Jim Thome walked and Abreu lined a 1-2 pitch into the right-field basket for a 5-3 Phillies lead.
A walk to Ricky Ledee and singles by Jimmy Rollins and Todd Pratt finished Wood. Kyle Farnsworth relieved and gave up a sacrifice fly, a two-run single and two walks, one to winning pitcher Vicente Padilla.
"That's where the game got away," Baker said after the Phillies completed a two-game sweep. "It was a frustrating day. We couldn't turn off the faucet in that one terrible inning.
"Have I seen enough of the Phillies? Yes, they have a good club."
The Phillies lead the league in breaking the hearts of fans on the road. A crowd of 40,377 watched Randy Wolf shut out the Cubs 3-0 on Wednesday night and 40,260 watched Thursday's rout. The Phillies are 8-0 in road games drawing 35,000 or more fans.
Sammy Sosa's towering two-run homer, his 21st this season, earned the Cubs a 2-0 lead in the first inning.
Pratt's solo homer made it 2-1 in the third, but newly acquired Kenny Lofton restored the two-run lead at 3-1 when he hit a sacrifice fly in the fifth.
Hee Seop Choi hit a three-run homer of Padilla in the seventh.
Wood (10-7) experienced some tightness in his back before the game, but he didn't blame that or Saturday's 130-pitch outing in the Florida heat for his sudden loss of effectiveness.
"My back was OK," Wood said. "But after the fifth inning, my slider wasn't working. The grand slam was off a slider."