Milwaukee slugger Ryan Braun left after the third inning with a sore right thumb, which has been a lingering problem for him. Still, the Brewers took the final three games of the four-game series.
Gennett's triple highlighted a four-run second inning and Gomez's homer in the sixth off starter Jonathan Pettibone was plenty of insurance for Lohse's first victory since beating San Diego on April 22.
Lohse (2-6) experienced minor hamstring tightness in his left leg after running the bases during his previous start Tuesday, but showed no ill effects. His only major hiccup was Humberto Quintero's first home run of the season, a shot into the Phillies' bullpen in right.
Lohse gave up four hits, walked one and struck out six.
Jean Segura, who came in leading the NL in hits with 82, singled home two runs in the seventh. Martin Maldonado added a solo homer in the eighth.
Jim Henderson, just back from a strained right hamstring, pitched a scoreless ninth.
Pettibone (3-2) allowed six runs, four earned, and four hits in 5 1-3 innings. He struck out four but walked two and hit two batters with pitches in his first career start against the Brewers.
Milwaukee got to Pettibone in the second and then again in the sixth.
Logan Schafer singled in the sixth and then Gomez hit the first pitch from Pettibone into the Brewers' bullpen in left for his 11th home run of the season. After Maldonado walked, Phillies manager Charlie Manuel brought in Jeremy Horst.
The Brewers scored four runs in the second.
Pettibone got in trouble right away by making an error. He misplayed a bunt by Gomez, who went to second on Yuniesky Betancourt's single. Pettibone then hit Maldonado with a pitch, loading the bases.
Gomez scored on Juan Francisco's grounder to first. Gennett, who made his major league debut Tuesday night against Oakland, tripled to right-center for the first two RBIs of his career. He scored on Lohse's sacrifice.