Just minutes into the second half, the Gunners were awarded a spot kick on a supposed pull inside the area and the striker slotted home.
Giroud becomes the 19th Arsenal player to reach the landmark, scoring 100 goals in his 238th game for the club.
The France international joined Arsenal in June 2012, arriving from Montpellier in a deal worth £12million.
Giroud nearly left the club over the summer, with Everton and Marseille keen, but opted against an exit after deciding his "story was not finished."
The 30-year-old scored his 99th goal in the remarkable 4-3 win over Leicester City on the opening day of the Premier League season and have now completed his century.