With one out in the Giants' 11th, Deivi Cruz and Mike Matheny each singled off Glendon Rusch (5-4). Michael Wuertz replaced Rusch, and one out later, Ellison rapped a single to center for the game-winner.
"You hate to play that long and lose," Cubs manager Dusty Baker said. "Greg pitched a great game for us. He gave us all he had. We had some opportunities there. A runner on third is haunting us, and it's been haunting us for a while."
Maddux's milestone came in the third. With a runner at second and two out, Vizquel fouled the first two pitches off Maddux. Flashbulbs popped on the next three pitches. The first two were balls, and then Vizquel was called out on strikes by home plate umpire Joe Brinkman.
"There was a guy in scoring position with two outs and I'm trying to get an out," Maddux said. "If you strike him out, that's good, but I think I got ahead with changeups, and missed with two fastballs in, and made a better pitch on the third try."
As Maddux walked off the mound, catcher Michael Barrett ran over to hug him along with the rest of his Cubs teammates. The right-hander, not one for hoopla, headed into the dugout, but did come out for a curtain call to acknowledge the cheering crowd of 39,002.
The fans were on their feet every time Maddux got a two-strike count on a batter.
"It was different," Maddux said of the crowd reaction. "I don't try to strike guys out, I never have. I've always tried to just make a pitch, but I found myself trying to strike somebody out and it took me out of my game a little bit. It was pretty cool on the mound pitching with that. You hear it -- believe me, you hear it. This is a great place to pitch and tonight was a big reason why. The fans here are super."
They apparently wanted to witness history. The start of the game was delayed two hours and 43 minutes because of rain. Maddux began the night with 2,998 Ks and didn't waste any time counting down to 3,000 as he fanned Giants leadoff batter Ellison.
"I was talking to someone and said, 'These people don't go home around here, do they?'" Cubs rookie Matt Murton said. "That's something you don't normally see. To have that kind of rain and that kind of delay and still have a packed house is unbelievable, and it shows you what the city of Chicago is all about."
Maddux is all about pitching. He's the first pitcher ever to win his 300th game and notch his 3,000th strikeout against the same team. Maddux picked up the milestone win last Aug. 7 in San Francisco. He's also the ninth pitcher to win 300 games and strike out 3,000, joining a list of Hall of Famers.
"It's pretty cool," Maddux said. "Not that many guys have done it. I remember when [former pitching coach and current bench coach] Dick Pole told me one day, 'Why don't you stop trying to strike guys out and just try to get them out? You'll probably strike out just as many guys, if not more.' He was right. I've always tried with two strikes to just make a pitch and get the guy out. You get a lot of strikeouts by accident just by doing that."
"It was pretty cool on the mound pitching with that. You hear it -- believe me, you hear it. This is a great place to pitch and tonight was a big reason why. The fans here are super."
-- Greg Maddux on cheering fans
He's also one of the few to reach 3,000 strikeouts with less than 1,000 walks. Ferguson Jenkins is the only pitcher to finish his career with those numbers.
"For me personally, it's nice to get there with the least amount of walks alongside Fergie," Maddux said. "That's kind of cool."
The 39-year-old right-hander flashed his Gold Glove in the sixth. The Giants had a runner at third and two out when Pedro Feliz hit a chopper in front of the plate. Maddux scooped the ball up on the run and was able to tag the baserunner out.
Maddux gave up two runs on eight hits over eight innings while striking out three to raise his career total to 3,001 Ks.
The Giants led, 1-0, in the fifth when Lance Niekro doubled to lead off, advanced on Matheny's single and scored on Noah Lowry's sacrifice.
Barrett doubled to open the Cubs' sixth, and two outs later, Murton bounced the ball to third baseman Edgardo Alfonzo. His throw skipped past first, Murton was safe on the hit, and Barrett scampered home on Alfonzo's error to tie the game at 1.
Niekro doubled to open the seventh and scored two batters later on J.T. Snow's pinch-hit single. But Barrett tied the game at 2 with a leadoff homer in the eighth off the first pitch from former Cubs pitcher LaTroy Hawkins.
The game started at 9:48 p.m. CT, the latest first pitch in Wrigley Field history. It seemed an even longer day because of the loss.
"It would've been a lot better if we had won that game," Baker said, "but you still have to congratulate Greg."
"You never want anything you do to take away from what the team's trying to accomplish," Maddux said. "It's about us being in a Wild Card race and putting us in a position to get to the postseason. It's not about one player, it's about what can we do to get to the postseason.
"You play the game to win, and we came up a little short," Maddux said, "so play better tomorrow."