Halladay (3-0) struck out six and allowed seven hits in eight innings on a crisp and cool spring night along the bay. He also had an RBI single in a rematch of aces from the 2010 NL championship series.
Laynce Nix's two-run double highlighted a four-run first off Lincecum (0-2) that produced all the power Philadelphia needed. The Phillies chased San Francisco's shaggy-haired and struggling right-hander after he gave up five runs and eight hits in six innings.
Jonathan Papelbon pitched a scoreless ninth for his third save in three chances this season.
A rare gathering between two of baseball's best never lived up to the billing.
The pitching matchup was the first regular-season meeting of multiple Cy Young Award winners since Johan Santana and Randy Johnson on May 16, 2009. It also was the first time Halladay and Lincecum - who split two matchups in the memorable NL championship series the Giants won in six games en route to a World Series title - faced each other in the regular season.
Only one still resembled an ace.
Lincecum, coming off the worst outing of his career, has given up more runs in the first inning this season (nine) than he did all of last (eight). Halladay had only been nicked for one run and seven hits total in home wins against Pittsburgh and Miami previously.
Philadelphia backed its ace with all the run support he needed before Lincecum could even record two outs.
Hunter Pence and Shane Victorino each singled home a run and Nix smacked a two-run double in the first to give the Phillies a quick 4-0 lead. By the time Lincecum recovered from the 30-pitch inning, the damage had been done.
Halladay worked out of a jam in the first, allowing only Aubrey Huff's sacrifice fly to right. The pitcher even lined a run-scoring single in the fourth.
After Lincecum's RBI grounder in the fourth sliced Philadelphia's lead to 5-2, Pence picked up Halladay with a leaping grab against the right-field wall on a slicing fly by Angel Pagan to save a run.
An announced sellout of 41,136 fans had little else to get excited for other than watching one of baseball's best.
Halladay baffled hitters with a mix of devastating fastballs and late-breaking curves. He struck out Brandon Belt looking with two on to end the fifth, and closed out the eighth in order after a leadoff single to Buster Posey.
The Giants suddenly have more concerns at the top of the rotation than its batting order.
Lincecum was tagged for six earned runs on eight hits and two walks in just 2 1-3 innings - the shortest outing of his career - in San Francisco's 17-8 loss at Colorado last week. He has allowed 16 runs and 22 hits in 13 2-3 innings this season.
NOTES: Giants 2B Freddy Sanchez complained of soreness in his surgically repaired right shoulder after a toss during an extended spring training game in Arizona on Monday. Manager Bruce Bochy said the team will push Sanchez's rehab start in Class A San Jose back at least two days to Thursday. ... A moment of silence was held before the game for the one crew member who died and four others still missing from the wreck of the yacht Low Speed Chase near the Farallon Islands off San Francisco on Saturday, including former Giants bat girl Alexis Busch. ... Phillies reliever Justin De Fratus, who had elbow soreness during at the beginning of spring training, threw about 30 pitches Monday against live hitters. He'll pitch again Thursday.