Bako scooped up the dribbler and fired it high over the head of first baseman Doug Mientkiewicz as the star shortstop motored on to second base.
The official scorer took a moment to rule the ball a hit and an error. When the crowd learned of the ruling it rose and began to chant, "Jeter, Jeter, Jeter."
The quiet Yankees captain stood at the bag and lifted his batting helmet as the crowd of 48,035, which included golfer Tiger Woods, continued to cheer as Yankees players hung over the railing in front of their dugout and applauded.
Unlike his mother Dorothy, Jeter said he would have ruled the ball a hit. But no matter whether it was a scorching liner or the tiny roller it turned out to be, the infielder said it was really no big deal to him.
"It's great, but we're trying to win games," Jeter said. "Personal accolades you look at when your career is over with, or when the season is over with. Right now, I wasn't concerned about it. The bottom line is we're trying to win."
Yankees manager Joe Torre said he knew Jeter would be uncomfortable having to stand on the diamond and tip his cap.
"Too bad we couldn't cap it off with a win for him," Torre said.
The Yankees were hoping Jeter would reach the landmark in his first at-bat, but he lined right-hander Scott Elarton's first pitch to right field for an out.
Jeter later walked twice and delivered a single up the middle in the seventh inning to bring his career hit total to 2,001.
Jeter became the eighth player to reach 2,000 hits as a Yankee, joining Lou Gehrig, Babe Ruth, Mickey Mantle, current teammate Bernie Williams, Joe DiMaggio, current batting coach Don Mattingly and Yogi Berra.
"It has been mentioned," Jeter acknowledged of the company he now keeps. "Anytime you are in the company of those names it feels good, but to be honest with you I wasn't sitting at home counting down to this day, or anything like that. My job here is to get hits, get on base and score runs. If you do that consistently, it means you have been playing for a long time. It's great, don't get me wrong."
Teammate Johnny Damon is impressed with Jeter's accomplishment.
"Anytime anyone can spend those number of years and is able to get that many hits, it's incredible," Damon said. "It's something every kid shoots for when he starts playing."