The Padres lost, 3-0, to the Giants on Sunday at AT&T Park in the season finale for both teams, only San Francisco advances to the postseason as the division champion.
"I've been in this game for 32 seasons, and this was one of the most rewarding," Padres manager Bud Black said. "It was a great year."
The Padres, a team whose success in 2010 was predicated on run prevention, pitching and defense, struggled mightily to score runs over the final five weeks of the season, a glaring deficiency that proved to be their downfall.
The Padres were shut out 12 times this season, with five of those coming in their last 23 games.
"The timely hitting, probably more than anything, [has been the problem]," Black said. "I think earlier in the year, we got a lot of clutch hits.
"We just haven't gotten guys on base at the rate that we did earlier in the year, so the less guys you have on, the less times you have to score. We had more opportunities earlier in the year, and we cashed in a little more frequently."
On Sunday, the Padres (90-72) managed three hits against six Giants pitchers.
San Diego, which started the season with the second-lowest payroll in the Majors, led the division for much of the summer until staggering down the stretch. The Padres led the NL West by 6 1/2 games on Aug. 25.
The Padres dropped 10 consecutive games from late August into early September and the Giants passed them, taking a three-game lead into the final weekend. The Padres won the first two games before falling on Sunday.
"We've got a lot a heart, never say no," said Padres reliever Heath Bell, who saved 47 games. "People can push us down, but we did a bunch of things that nobody thought we could do.
"Even though we didn't get to our main goal, we proved some people wrong and we learned what a lot of our young guys are made of, and they're made of winners. We've got a lot of winners in this clubhouse. We just didn't come out on top."
Despite the loss, the Padres reached the 90-victory mark for the fourth time in the history of the franchise. The 90 victories also represented a 15-game improvement from the 2009 season.
"San Diego, what a year they had. I want to compliment them. What a year they had," Giants manager Bruce Bochy said. "They surprised everybody, and Buddy and his staff did a tremendous job there. Nobody saw them playing in a game today like they played."
All of this wasn't expected from the Padres, who operated with a limited budget under a first-year general manager, Jed Hoyer, who was still getting acclimated to the organization.
But Hoyer made a few smart moves in free agency, signing Jerry Hairston Jr., Jon Garland and Yorvit Torrealba and signing Chris Denorfia and Matt Stairs to Minor League contracts.
"It's been great to watch these guys play, even going back to Spring Training. The energy level was so high," Black said. "I don't like to make predictions, but I felt good about our team.
"A lot of our players had great years and played great baseball."