Biggio met the 15-year-old Frankie Velasquez through his work with The Sunshine Kids Foundation, an organization which helps children with cancer, when Velasquez was 6 and has kept in touch with him since.
"He's one of a kind," Velasquez said. "He's done so much for us Sunshine Kids and I'll always be grateful to him. Seeing this happen was a once in a lifetime experience."
Lee's drive to left field off Brian Fuentes (0-3) came on the first pitch. Biggio singled in the 11th
-- for just his second career five-hit game -- and Hunter Pence followed with a double before Lance Berkman was hit by a pitch to load the bases.
"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."
In other NL games, it was Los Angeles 9, Arizona 5; Philadelphia 8, Cincinnati 7 in 10 innings; and Florida 9, Pittsburgh 7. St. Louis' game at the New York Mets was rained out.
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Troy Tulowitzki's solo shot off Brian Moehler (1-2) to lead off the 11th inning made it 5-4. The loss extends Colorado's season-high losing streak to seven games.
Biggio became the 27th player to reach the mark with his single to center in the seventh inning. The 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.
"I couldn't have scripted it any better," Biggio said. "There are a lot of things that have happened over the past 20 years but tonight is the best."
Biggio is the first player to reach 3,000 hits since Rafael Palmeiro on July 15, 2005, with Baltimore. He passed Roberto Clemente for 26th on the career list with his fourth hit, a ninth-inning single.
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.
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Biggio's milestone 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 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'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."