SAN FRANCISCO -- For many in the organization, including managing partner Peter Magowan, Barry Bonds' first home run as a Giant at Candlestick Park will remain singular in memory.

It happened the first time he stepped in the batter's box at Candlestick in 1993, cutting through the cold air.

On Wednesday night, 15 seasons after he revitalized a franchise, Bonds couldn't exit with the same punctuation. He slapped his bat with his hand immediately after hitting a fastball from Jake Peavy that died at the warning track.

Six innings, three at-bats, two tappers on the infield and a final fly ball to the track. Then it was time to say goodbye.

Like a perfect showman, Bonds kept them wanting more.

A decade and a half after coming home to the team of his boyhood, 50 days after surpassing Hank Aaron as the all-time home run king and a week after the Giants informed him that he wouldn't return, Bonds waved farewell to a sellout crowd of 42,926 at AT&T Park.

In their home finale, the Giants lost 11-3 to the San Diego Padres, who retained a one-game lead over Philadelphia and Colorado in the National League wild-card standings.

The Giants are not part of the playoff race for the third consecutive season. But the franchise mostly enjoyed high moments and winning records in Bonds' era, which began with a record-setting contract at the 1992 winter meetings.

"With that move, we were able to revitalize interest and make this a baseball town again," said Magowan, his eyes moist in the postgame clubhouse. "Say what you want to say about Barry, but he was part of winning baseball teams. He made the people around him better. He helped us win. That's what we're in this game to do, and we did win. I feel great that we were able to do that."

Playing for the first time since Sept. 15, Bonds couldn't hit the ball out of the infield in his first two trips against Peavy, the leading Cy Young Award contender in the NL. Bonds limped after balls in left field on his sprained toe.

But he remained in the game for one more at-bat, and once the Padres built a comfortable lead, Peavy was free to throw him straight heat. Bonds hit a 2-0 pitch to right-center and the crowd gasped, but the 43-year-old slugger instantly recognized he didn't get all of it.

"Just missed it," Giants manager Bruce Bochy said. "He wanted to go out the right way. He was in pain. He had to run a lot in the outfield. It couldn't have been easy, but it sure didn't show for him."

The fly out ended the inning, and Bonds wrapped his arms around Peavy. Then he waved to the crowd and descended into a church-silent dugout where teammates met him. Bonds' lips never quavered, but first baseman Ryan Klesko saw emotion on his face as he shook his hand.

"This was brought on him pretty quick, the last homestand of the series, and it hit him hard," Klesko said.

Bonds waited almost a minute as the crowd chanted his name before trotting out for a curtain call. Then he grabbed his bats and headed down the tunnel, where his family met him at the clubhouse door.

The left-field bleachers were a mix of signs, flashbulbs and hero worship. The fans stood and applauded Bonds each time he jogged to left field, and he acknowledged them with a wave or a waggle of his cap.

A hopeful armada of kayaks and dinghies gathered in McCovey Cove for one last attempt to claim waterlogged history.

Club officials painted Bonds' name and number at his spot in left field. He was forced to vacate that space often as he limped after a flurry of hits, and was charged with an error when a bouncing ball popped out of his glove.

"I'm sure he wished he hit three home runs in three at-bats," Magowan said. "But he was hurting. He was a little afraid if a ball was hit out there, he wouldn't make it."

Bonds is not the same all-around force that the Giants signed away from Pittsburgh prior to the 1993 season, but he led the major leagues in walks this season and his average of one homer per 12.14 at-bats ranked third in the NL, behind Milwaukee's Prince Fielder and Philadelphia's Ryan Howard.

The son of Bobby Bonds and godson of Willie Mays, Bonds won five of his unprecedented seven NL Most Valuable Player awards as a Giant, and five of his eight Gold Gloves. He was an All-Star 12 times as a Giant -- including this season, when he was the only player to represent the host franchise at AT&T Park.

And Bonds was good for the bottom line. With his star power, the Giants sold everything from the big stuff (season-ticket packages, luxury suites) to the small stuff (rubber chickens).

Yet it came at a price beyond the millions Bonds earned over the years. The franchise dealt with constant Bonds-related headaches, including the BALCO steroid controversy.

The Giants played Bonds' career highlights between each inning. After the game, they played a video tribute set to Frank Sinatra's "My Way."

Giants players tossed autographed balls into the stands, but Bonds did not appear. The fans had gotten their last glimpse.

"There's nothing like it," Bonds told MediaNews earlier this month. "Nothing like it in the world. It's your home. ... I lived a perfect childhood dream starting with Willie and my dad, having an opportunity to play here."

Contact Andrew Baggarly at abaggarly@mercurynews.com.