Hundley also provided the only run against Lincecum, hitting a solo home run into the second deck in left field in the third inning of San Diego's 8-4 loss. It was his first.
Lincecum struck out 13 and held the Padres to one run and three hits in seven innings.
Hundley is batting .500 and has at least one hit in all five games.
"We saw it in spring training," manager Bud Black said. "I think he knows what's ahead of him this season. I don't want to get ahead of ourselves here, but he's got a nice start, a nice first week. He's playing very good baseball right now."
Veteran Gregg Zaun, slated to back up Hundley, retired during spring training. That helped cement Hundley's status as the No. 1 catcher.
Lincecum left with an 8-1 lead after seven. Closer Brian Wilson, activated from the 15-day disabled list before the game, pitched the ninth in a non-save situation, allowing three runs on two infield singles and a walk.
The Padres made it interesting in the ninth. After Jeremy Afield relieved Wilson, Chase Headley hit a two-run double over center fielder Andres Torres' head. Ramon Ramirez came on with the bases loaded and two outs and got Rob Johnson to fly out to center, earning his first save of the season.
The defending World Series champion Giants won for just the second time in six games.
Lincecum struck out 10 or more for the 27th time, tying Jason Stemmed for the second-most by a Giants pitcher since 1900. Christy Mathewson did it 28 times. Lincecum, the NL strikeout leader the past three seasons, has done it four times against the Padres, all at Petco Park. His career high is 15.
Baffling the Padres with sliders, splitters and fastballs, Lincecum struck out Brad Hawpe three times.
Lincecum (1-1) didn't walk a batter and left with an 8-1 lead after seven. He was the hard-luck loser in the season opener Thursday night at Los Angeles, when he allowed an unearned run in a 2-1 defeat.
The Giants' 3-4-5 hitters, Aubrey Huff, Buster Posey and Pablo Sandoval, had three hits apiece. Posey hit a two-run homer and a two-run single, while Huff had a pair of run-scoring doubles and an RBI single.
The Giants gave Lincecum a 3-0 lead in the first. Freddy Sanchez hit a one-out triple to right-center and Huff brought him in with a double to right. Posey followed with his first homer of the season, to left on a 3-1 pitch from Tim Stauffer (0-1).
The Giants chased Stauffer in the fifth, two batters after he allowed Huff's RBI double to left-center. San Francisco batted around in the sixth and added four runs against San Diego's bullpen. Huff hit a bases-loaded infield single, Posey followed with a two-run single to right and Sandoval's RBI hit to right.
Stauffer allowed four runs and eight hits in 4 2-3 innings, walked two and struck out one.
NOTES: Lincecum is 6-3 with a 2.03 ERA in 14 career starts against San Diego. ... The Giants are off Thursday, then play their home opener Friday afternoon against St. Louis. ... Padres lefty reliever Joe Thatcher, on the DL with a strained left shoulder, had a setback and won't pick up a ball for the next four or five days. ... Padres ace Mat Latos, on the DL with a sore right shoulder, threw a bullpen. He's expected to rejoin the rotation for a series against Cincinnati that starts Monday night.