Rookie reliever Roberto Novoa walked in the winning run with two outs in the ninth inning of a 4-3 loss to the Brewers, as the Cubs let another winnable game slip away.
"Boy, we're losing all kind of ways," Baker said. "We have got to keep on fighting."
The Cubs dropped two games under .500 and into third-place in the National League Central, six games behind the division-leading Cardinals.
Damian Miller's bases-loaded walk off Novoa gave the Brewers their sixth straight win, while the Cubs have lost four in a row.
After Brady Clark's solo home run off Ryan Dempster gave the Brewers a 3-2 lead in the seventh, the Cubs tied it in the eighth when Derrek Lee singled, stole second and scored on Michael Barrett's RBI single.
But the trouble began in the ninth when Milwaukee's Bill Hall doubled off Novoa with one out.
After an intentional walk to Geoff Jenkins, Hall advanced to third on a fly to right by Carlos Lee. Lyle Overbay was intentionally walked to load the bases with two outs before Miller walked on a 3-2 pitch to end it.
Baker left closer LaTroy Hawkins sitting in the bullpen, opting to stick with the rookie in a tie game.
"I thought the kid had the best shot at getting those guys out that were coming up," Baker said. "We were saving 'Hawk' in case we got the lead, for the save. We had a lot of opportunities, especially in that first inning."
The Cubs had runners on first and third with no outs in the first but failed to score, a recurring theme this season.
Although the Cubs came into Wednesday ranked fourth in the National League in runs scored and batting average, they've also developed a nagging tendency to shut it down during the late innings. The Cubs are batting a combined .229 from the seventh inning on, suggesting a lack of clutch hitting from all involved.
Dempster pitched well in his first start in a week, holding the Brewers to three runs on six hits in 6 2/3 innings. But the Cubs have scored only eight runs for Dempster while he has been in the game during in his six starts.
"Right now, nothing is really falling our way," Dempster said. "We just have to keep battling. We're playing good baseball. We're just coming up short a couple times, and that happens."
Baker inserted Aramis Ramirez in the No. 3 hole for the second straight day, hoping the presence of Lee in the clean-up spot would ensure better pitches for Ramirez.
"I know he's going to hit," Baker said. "We're just trying to relieve some pressure off of him and help him. When you're stroke is off, you're late on fastballs and you're early on breaking balls. That's where he is right now."
Ramirez stranded runners in both the first and seventh innings, but had a pair of hits, including a leadoff double in the sixth that led to the go-ahead run. Ramirez advanced on Lee's fly to deep right, then scored on Jeromy Burnitz's single.
St. Louis' 7-3 win over Cincinnati was on the board and staring down the Cubs in the late innings.
"You don't want nobody to go run away and hide," Baker said. "It's up to us to start winning. Even though you look at the scoreboard and hope they lose every day, it really doesn't help the situation. You just have to take care of what you've got to do. That's the whole secret."
psullivan@tribune.com