"I think it was the way it was supposed to be done," Biggio said as he choked back tears. "To have it happen here -- that was a special atmosphere that was out there today."
Lee's shot to left field off Brian Fuentes (0-3) came on the first pitch. Biggio singled in the 11th, and Hunter Pence followed with a double before Lance Berkman was hit by a pitch to load the bases.
It was the third time in seven days Fuentes has allowed a game-winning hit after Tulowitzki homered in the top of the inning to give the team a late lead.
Biggio became the 27th player to reach the mark with a single to center field in the seventh inning. The Astros second baseman was thrown out trying to stretch the play into a double on his third hit of the night, which tied the game at 1.
He added his fourth hit on a single to right field in the ninth for hit No. 3001 and his first four-hit game of the season.
Biggio is the first player to reach 3,000 hits since Rafael Palmeiro on July 15, 2005, with Baltimore.
The 41-year-old, who entered the season needing 70 hits to reach the milestone, has played his entire 20-year career with the Astros, making him the longest tenured player in franchise history.
"This was just unbelievable the way it all came down," said Astros owner Drayton McLane. "We tied the game and then we lost the lead, then the grand slam. We'll all remember this the rest of our lives."
Dan Wheeler pitched a perfect 10th for Houston, striking out all three batters.
The game was tied at 1-all in the eighth when Ryan Spilborghs followed a double by Garrett Atkins with a home run to right center field to make it 3-1. A single by Chris Iannetta later in the inning score Tulowitzki.
Houston tied it again when Berkman and Mike Lamb homered in the eighth inning. Berkman's was a solo shot to left field and Lamb's a two-run homer to right-center field.
Ianetta's solo homer to left field in the third inning gave Colorado a 1-0 lead.
Biggio entered the game needing three hits to reach 3,000. The first came on a single to center field in the third inning.
The second hit, also a single, came on a grounder to third in the fifth. Atkins badly overthrew first base on the play, leaving the official scorer to pause for several tense seconds before calling it a single and ruling an error that allowed Biggio to advance to second.
The sellout crowd stood and chanted 'Bi-ggi-o' at each bat and cameras twinkled with each pitch. Fans held signs that read 'Mr. 3,000' and 'Biggio's Hit Parade.' One woman wore an orange shirt that featured block letters that read 'Biggio' and '3,000.'
His 3,000th hit came one day shy of the 19th anniversary of his first career hit, a single off Orel Hershiser on June 29, 1988.
Fireworks went off, the counter in left-center field with red illuminated numbers ticked to 3,000 and a giant banner with his picture and 3,000 that spanned from the train track to the roof of the stadium was unveiled after the hit.
He dragged Jeff Bagwell, a teammate of his for 15 seasons, onto the field after reaching the mark. After all the two went through together, he wanted to share the moment with him.
"I wanted him on that field, between the lines one more time with me to really let the fans say goodbye, say hello, say thank you for so many things," Biggio said. "To me that was what it was about. He deserved it and I deserved it in a way. I just wanted him to enjoy it and be happy one more time with me."
Bagwell was moved by the gesture.
"I'm just so proud of him," Bagwell said. "I just want everyone to appreciate that that's the kind of person he is off the field as well the kind he is on it. I'll never forget this moment."
Rockies manager Clint Hurdle said there is no opposing player he'd be happier for in this situation than Biggio.
"He's good for baseball," Hurdle said. "He's been good for the Astros organization. It was very fitting for it to happen at home in front of a packed house."
Houston ace Roy Oswalt allowed nine hits and walked two with four strikeouts in seven innings.
Colorado starter Aaron Cook allowed seven hits and one run with two strikeouts in seven innings.
A scary moment came in the fourth when Lee was hit in the head with the ball while stealing second when Tulowitzki mishandled a throw from Ianetta. He fell to the ground and looked dazed for a few moments while trainers attended to him, but remained in the game.
- Thursday's game was the third extra-inning game in the last five days for Houston.