The marquee striker netted the match winner from the spot in the 85th minute after she was awarded a contentious penalty going to ground on the edge of the box.
Kerr had turned Canberra defender Karly Roestbakken before going down after a shoulder to shoulder duel on the edge of the penalty area.
It proved to be the only goal of the match as the Glory took home all three points as they claimed their second win in three games.
Perth moved into equal first on 16 points alongside Melbourne Victory,
It was a frustrating contest for both sides with neither Perth or Canberra unable to create any true chances in a tightly fought opening 45 minutes.
Kerr had the best chance of the opening stanza when she fired wide after connecting with a curling corner kick at the back post.
Perth picked up the pace in the second half with striker Rachel Hill combining with Kerr to create plenty of headaches for the Canberra defence.
A moment of brilliance from Perth goalkeeper Eliza Campbell stopped United taking a shock lead when she tipped a Nickoletta Flannery thunderbolt over the crossbar with an incredible acrobatic save.
With the game on track to end as a dour scoreless draw, Kerr found her self with only one defender to beat after receiving a long ball over the top from Hill.
Kerr took on Roestbakken and went down as they battled for the ball.
Perth's top goalscorer wasn't going to miss from the spot and fired into the bottom left corner to secure the win.
