With the game approaching marathon length, Manuel needed an outing out of Gordon before turning the game over to Clay Condrey, the last man standing.
Gordon delivered, and understood the manager's position.
"I still feel a little rusty," Gordon said on Wednesday. "I'm trying to stay with the program they have me on. Every day, I feel like I'm taking some giant steps. I just have to stick with it.
"That first game in Los Angeles, I was skeptical. The second game I felt a lot better, as far as command. Last night was a big step for me because I felt like I was in control of every pitch. I haven't felt like that since last year. I felt like I was really under control."
Gordon was warming in the ninth inning, and got up again before pitching the 11th.
"I was starting to get myself prepared," Gordon said. "I still have some time where I feel good some days. Yesterday, it just took me longer to get a feel, so I needed to throw for a little bit, and I got up a couple of times before I got in the game."
1,000 for Mesa, adventure for Helms:
Jose Mesa's 1,000th career appearance was a loss.
The veteran closer, who has pitched to many Hall of Famers in a 19-year career and three father-son combinations -- Cecil and Prince Fielder, Ken Griffey Sr. and Jr. and Jesse and Josh Barfield -- relieved J.C. Romero with two outs in the sixth inning. He struck out Ronnie Belliard and got the ball from catcher Rod Barajas.
It didn't go as well in the eighth, when Wes Helms committed an error on Ryan Zimmerman's grounder leading off the inning, then slipped as he tried to turn a double play on the next hitter, losing his shoe as he fell. He got a force at second, but felt he would've gotten two had he made a clean throw.
"I don't know how it went that far," Helms said. "When I spun, my right foot was planted and when the shoe came off it made my foot come out from under me."
On the ball Zimmerman hit, Helms blamed his footwork.
"When your feet aren't underneath you, you're either going to throw the ball down or up," he said. "My feet weren't in a good position, which made me throw the ball down. I busted it off the bat. ... My feet were never in a good position."
Mesa walked the next hitter, and was saddled with the loss when Mike Zagurski gave up a three-run home run to Jesus Flores.
That was a long one: Carlos Ruiz said it with a straight face ... at first.
"I felt the same," he said, asked how he felt catching Clay Condrey's final pitch in the 14th inning on Wednesday, as opposed to Cole Hamels' first offering in the first inning. Then, he laughed.
"I was a little tired," Ruiz said. "I don't remember [catching] a longer game."
Ruiz caught 231 of the game's 446 pitches on Wednesday night. He went 0-for-5 at the plate, continuing a July slide in which he's batting .146. Though he would like to be more productive offensively, he'll take an extra-inning win.
"I'm swinging too hard right now, and trying to do too much at the plate," he said. "But if we win and the pitcher throws a good game, that's OK with me."
Lefty Jamie Moyer takes on the Pirates on Friday night at 7:05 ET in the opener of a three-game series. Moyer beat San Diego's David Wells on July 21, picking up his first win since June 22. The drought had lasted four starts and included three straight losses, one of which saw him allow 10 earned runs to the Dodgers. Moyer was more consistent against the Padres, lasting 6 2/3 innings and giving up four earned runs. He has a 5.22 ERA lifetime against the Pirates in 10 career starts.