City had looked set to grab a well-deserved first point in their second match of the campaign against the Japanese champions following their 2-0 home defeat to another J1 League powerhouse, Sanfrecce Hiroshima, a fortnight earlier.
When the home side's goalkeeper Shuichi Gonda hoofed a long ball downfield in the 94th minute in Kobe on Wednesday, there had initially looked little concern despite the ball being flicked on towards the City defence.
Even when the ball was worked through towards striker Koya Yuruki, it appeared that City keeper Patrick Beach would get to the ball before him and clear his lines.
Instead, Beach's attempted clearance only rebounded off the back of his teammate Samuel Suprayen and fell, cruelly, straight into the path to Yuruki, who could hardly believe his luck as he hammered the ball home into an empty net.
"I think for the majority of the game we were in it, we were doing well and up until the minute we conceded the goal we were competing well," said dismayed City captain Aziz Behich.
"I'm proud of my players. They competed for more than 90 minutes and it just hurts the way we conceded that goal in the last minute."
So, City are now the only team in their 12-strong 'east' league who are still without a point after the first two rounds, so they're already playing catch-up with only eight of the dozen able to qualify for the next phase.
Kobe, in contrast, have maximum points and lead the standings.
City had named eight of the team who'd lost against Hiroshima, but manager Aurelio Vidmar was without Mathew Leckie due to injury, the Socceroo being replaced in the starting XI by Emin Durakovic.
Elsewhere in the group on Wednesday, twice winners Ulsan HD from South Korea drew 1-1 with China's Shanghai Shenhua and are now just two points behind leaders Kobe.
Hiroshima and FC Seoul are also on four points with Gangwon FC, Chengdu Rongcheng and Buriram United a further point behind.
