SAN FRANCISCO – Early Wednesday, Tim Lincecum was alternately sharp and vulnerable.

He struck out three San Diego Padres in the first inning, but he left a pitch up that Chase Headley lofted to left-center field for a home run. He issued a one-out walk in the second, then took control of the inning, striking out the next two batters.

That delicate balance didn't last.

Working on a high pitch count, Lincecum failed to get out of the fifth inning in his first rough outing of the second half of the season as the Giants fell short of sweeping the Padres with a 6-3 loss in the series finale.

For Lincecum (4-11), who had allowed two runs in 15 innings since the All-Star break, taming the up-and-down nature of his season remains an issue. The right-hander has yet to string together three quality starts and had little room for error anyway Wednesday, with Padres starter Jason Marquis holding the Giants to one hit through six innings.

Before the game, manager Bruce Bochy jokingly referred to his lineup, which was missing several regulars, as the "bomb squad." By the time the Giants made some noise in the late innings, Lincecum's day had long been over.

"He ran some deep counts and it caught up with him, I think," Bochy said. "I thought he had good stuff. I thought he came out and looked crisp, had a good fastball going. … I thought more than anything the pitches caught up with him today."

Lincecum, who struck out six of the first 10 hitters he faced, said he started to struggle with pitch control as the game went on, particularly with his fastball.

"I think execution of my fastball kind of made the difference," he said. "I think early on, with the exception of that pitch to Headley, my fastball just kind of got away from me and I wasn't hitting the spots I needed to."

Lincecum seemed particularly irked by a one-out walk to Everth Cabrera that loaded the bases in the fourth. Lincecum struck out Marquis for the second out, but Will Venable cued a ball to shallow left-center that eluded a diving Angel Pagan by inches for a two-run double.

That hit, Lincecum said, "kind of made the difference in the game."

The Padres added two runs off Lincecum in the fifth on a loud homer by right fielder Jesus Guzman, who also hit a solo shot off Brad Penny in the eighth.

After Gregor Blanco led off the first inning with a single, eventually scoring on Melky Cabrera's sacrifice fly, the Giants didn't have another hit until Pagan doubled with two out in the seventh.

Despite a stretch in which Marquis retired 16 straight hitters, the Giants brought the tying run to the plate in the eighth.

Ryan Theriot's two-out RBI single cut the deficit to three and brought up Cabrera with runners on first and third. But Cabrera struck out swinging against closer Huston Street, who had come in to face the Giants' best hitter.

Notes – An MRI confirmed a hamstring strain for Pablo Sandoval, Bochy said. The Giants, though, plan to see how Sandoval responds to treatment and will wait until Friday to decide whether to place him on the disabled list. Sandoval was injured stretching for a throw at first base Tuesday.

• Bochy sat catcher Buster Posey, giving him two days rest with today's day off before a three-game series against the Los Angeles Dodgers. Eli Whiteside took over behind the plate.

• Backup catcher Hector Sanchez, recovering from a left knee sprain suffered last week in Atlanta, is scheduled to start a rehabilitation assignment at Triple-A Fresno today, Bochy said.

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