Ultimately, the difference was Anthony Rizzo's two-run, first-inning homer off Ryan Vogelsong nearly 48 hours after the game actually began.
But subsequent events overshadowed Rizzo's drive.
The Giants received a second chance to win this game, as the Commissioner's Office upheld their protest of what was initially a rain-shortened, 2-0 Cubs victory. The Giants successfully maintained that the grounds crew's deployment of the Wrigley Field tarpaulin was flawed.
It marked the first time since 1986 that a club's protest proved effective. The Giants did virtually all they could to seize their opportunity.
Trailing, 2-1, they began their ninth-inning surge with one-out singles by Joe Panik and Brandon Crawford off Chicago closer Carlos Rondon. Panik's hit was his fourth in a row since Wednesday. Third baseman Luis Valbuena nearly speared Crawford's liner, but it grazed his glove.
Rondon recovered by striking out pinch-hitter Gregor Blanco. Up came Pagan, who smacked a 1-0 fastball back at the right-hander. The ball initially appeared destined to scoot into center field. But it struck Rondon, who couldn't find the ball immediately and fumbled around for it. However, he quickly realized it was within easy reach and underhanded his throw to first base, ending the saga.
"We all thought when Pagan hit the ball it was going through," Giants manager Bruce Bochy said.
Indeed, a Giants comeback seemed inevitable, if only because they controlled the action upon the game's resumption in the bottom of the fifth inning.
Fittingly, showers halted the game's start for one hour, 57 minutes, bringing the total delay -- including Tuesday's game-ending stoppage -- to 6:31.
Coming off Wednesday's 8-3 victory, the Giants maintained pressure by scoring with two outs in the sixth. Adam Duvall's double off the left-field wall prolonged the inning for Panik's RBI single.
Yusmeiro Petit "started" for the Giants and led a superb relief effort, striking out the first five batters he faced in two perfect innings. He, Jean Machi and Jeremy Affeldt combined to no-hit Chicago for four innings.
But the Giants still absorbed their 11th defeat in 18 one-run games on the road. They outhit Chicago, 11-3, but went 2-for-9 with runners in scoring position.
"It's over now," Bochy said, punctuating the adventure that preoccupied two teams, their respective front offices and multiple Major League officials. "All we wanted was a chance, and we got it."