"We'd have had to waste another hour and a half, two hours," Guillen said. "It's not in my hands. The umpires say, 'We're not going to wait that long.' They had the power to do it. They did the right thing, not keep us here until 1 o'clock in the morning and then bang it. ... I think they did what they had to do. Unfortunately, we were down on the scoreboard."
The Marlins are now 3-3 since the All-Star break, and they can still take the series at Wrigley Field with a victory on Thursday afternoon.
In a four-run seventh inning, Josh Johnson saw a splendid outing turn into a disheartening loss.
Geovany Soto chopped a go-ahead single off Johnson and Jeff Baker ripped a two-run double off Mike Dunn. David DeJesus's sacrifice fly provided some additional insurance, and the Marlins had their two-game win streak snapped.
Johnson (5-7) was charged with four runs on five hits in 6 1/3 innings.
"It's really frustrating," Johnson said of the team not sustaining a winning streak. "That's what you've got to do, you've got to string together wins, and I just didn't come through for the team."
Jose Reyes homered for Miami, but the team wasted early chances off Jeff Samardzija, putting runners in scoring position in three of the five innings he pitched.
"Once again, we're not bringing those guys in," Guillen said.
The Marlins were 0-for-8 with runners in scoring position, and they left 11 on base.
Emilio Bonifacio had a single, double and triple on the night, and the Marlins continue to never have had a player hit for the cycle.
In the seventh, Alfonso Soriano reached on an infield single. Second baseman Omar Infante made a nice backhanded play on Soriano's grounder up the middle, but his off-balanced throw pulled Carlos Lee inches off first base.
The hit came after Soriano lifted a foul ball behind the plate that barely cleared the screen. Given new life, Soriano was able to get the rally started.
A wild pitch advanced Soriano to second, and he moved to third on Bryan LaHair's groundout to first. With the count full, Soto chopped an RBI single just over the reach of a leaping Hanley Ramirez at third base, giving the Cubs a 2-1 lead. After Darwin Barney slapped a single just out of Ramirez's reach, Johnson was replaced by Dunn.
"Things were rolling along, I was getting early contact," Johnson said. "I was getting ahead, for the most part. But then, they get a chopper and a bloop. Nothing you can really do about it."
With the bases loaded, Baker added his two-run double, and DeJesus lifted a sacrifice fly to center.
Samardzija lasted five innings, giving up one run on six hits with nine strikeouts. Miami succeeded in running up the right-hander's pitch count to 97, causing him to be lifted for a pinch-hitter in the fifth.
"The Marlins make me throw a lot of pitches every time I face them," Samardzija said. "They got me down there. Kudos to the top of that lineup. When you put Bonifacio and Reyes back to back, as a pitcher, you really have to make sure you keep those guys off the bases.
"Not only are you trying to get good hitters out like Carlos Lee and Hanley and those guys, but you're also worrying about the guy on first base. It really causes a problem. I was happy with how I managed the game and made pitches with runners on the bags."
Reyes led off the third inning with his fourth home run of the season. The blast to right off Samardzija extended Reyes' hitting streak to six games.
Miami had three hits and a walk in the inning, but couldn't capitalize any more. Bonifacio, who singled, was thrown out at second attempting a delayed steal.
The first hit Johnson allowed came on his first pitch of the fourth inning. It was a costly one, as Starlin Castro blistered a game-tying home run to left-center.
The Marlins wasted a scoring chance in the fifth after Bonifacio led off with a triple. With the infield in, Lee grounded out to short. Miami caught a break on Logan Morrison's grounder to first. Bonifacio was in a rundown, but catcher Soto dropped the ball.
At the time in a 1-1 game, it appeared to be the break the Marlins needed.
Miami had second and third with one out, but Ramirez struck out looking and Greg Dobbs tapped a slow grounder to first.
"We got a break when Soto dropped the ball," Guillen said. "I was like, 'The ball is bouncing our way.' But nothing happened. That changed the scenario. And then the wild pitch [by Johnson in the seventh]. The wild pitch put them in scoring position. The next guy hit a ground ball, and we could have gotten out of the inning."