Showing no bad effects from the bruised knee that forced his last start, Lincecum (13-3) allowed three hits, one run and four walks while striking out 10 — five with runners in scoring position.
San Francisco manager Bruce Bochy pulled his ace after Chipper Jones' single gave the Braves two baserunners in the eighth. Reliever Jack Taschner allowed an RBI single to Mark Kotsay, the first batter he faced, and Bochy brought in Wilson.
Wilson, who pitched the ninth to earn his NL-leading 33rd save in 35 chances, intentionally walked Brian McCann before ending the eighth on Jeff Francoeur's fielder's choice grounder.
Travis Ishikawa's first career homer, a two-run shot in the second, opened the scoring. San Francisco led 3-0 in the fifth when Randy Winn tripled and scored on Emmanuel Burris' RBI single.
Rookie Charlie Morton (3-7) remained winless in seven starts at Turner Field after giving up seven hits, three runs, two walks and six strikeouts in his first career appearance against the Giants.
The Braves have lost five of six.
Lincecum is now 12-2 in 21 starts that follow a loss for San Francisco, which had dropped five of six. The right-hander lowered his road ERA to 1.88, best in the majors, as the Giants improved to 9-1 in his 13 starts and one relief appearance away from home.
Despite taking a liner off his knee in Houston and leaving his previous start Tuesday after 4 1-3 innings, Lincecum had a fluid delivery and lost none of his accustomed velocity, which was still around 95 mph in the eighth.
After Kelly Johnson singled with one out in the second, Lincecum held the Braves hitless until Yunel Escobar's leadoff double in the sixth.