Absent for nearly two years with an ACL injury, striker-captain Kerr notched her 70th goal for the 'Matildas' and first since an Olympic qualifier against Taiwan in the same city in November 2023.
Kerr's 14th-minute strike was a delight for home fans among the crowd of 44,379, a record attendance for a Women's Asian Cup match, but it proved the sole highlight in a match where the Matildas blew chances and the 41st-ranked Philippines defended in numbers.
"I think I'm just finding my confidence again," Kerr said of her long lay-off with injury.
"I feel like I'm still my normal self, I've just got to get more touches in and around the box.
"Today was a good start and there's a lot of belief in the team but as you see today, there's a lot of quality teams in the Asian Cups so you have to take it one day at a time."
Australia routed the Philippines 8-0 in their previous match during Olympic qualifying in 2023 but the hosts were well-held on Sunday, even if the Southeast Asians failed to record a single shot on goal.
Clare Hunt broke the game open with a deep cross from the right corner to the far post, finding Caitlin Foord who headed the ball down for Kerr to nod in from close range.
Emily van Egmond could have doubled the score with another header from the same spot minutes later but sent it flying over the bar, while Hayley Raso's well-taken volley into the net was chalked off by the VAR for offside on the half-hour mark.
With Australia continuing to rack up shots on goal after the break while conjuring few on target, coach Joe Montemurro subbed on Mary Fowler for the last 20 minutes to try to unlock their Group A rivals.
On the comeback trail from her own knee injury, the skilful Fowler had some nice touches but could also find no way through the wall of blue Filipina defenders.
Australia face Iran at Gold Coast Stadium on Thursday in their next group match, with the Philippines meeting South Korea in a double-header at the same venue.