Phoenix winger Carlo Armiento was given a red card in the 38th minute of their A-League Men clash after a brilliant opportunistic goal by Nigerian striker Ifeanyi Eze.
Down a man, Kazuki Nagasawa added a second in the 58th minute after a wonderful Eze counter-attack to break the hearts of the sold-out crowd.
Paulo Retre came off the bench to score in the 91st minute to secure a magnificent rearguard victory for coach Giancarlo Italiano.
"That was probably the best victory I've ever had as a coach. We've had it very hard," Italiano said, before welling up with emotion.
"I've been around a long time and heard a lot of crap, especially around the team. I'm just immensely proud for the group.
"They demonstrated everything today. It was almost like the football gods wanted Carlo to be sent off for us to go through this lesson."
Valkanis was serving a one-match suspension and was not permitted to be in the dressing room before the match or on the sideline during play.
Assistant coach Borja Lema stepped up but it was not an afternoon he will remember fondly.
Valkanis was sitting in a box on the eastern side of the ground and he would not have liked what he saw.
"We are unhappy with the result because we brought here a lot of fans we wanted to make happy. We were off today," Lema said.
"We will repay (the fans). We will make sure that happens."
Lema said he had good communication with the side's analyst and staff despite Valkanis's absence from a hands-on roll.
"We didn't lose today because Michael wasn't here but of course he has a big impact on the team because he is the leader," he said.
The Phoenix, 10th before the match, moved into eighth while the third-placed Roar threw away a golden chance to provisionally go top of the table.
The visitors stunned the Roar in the sixth minute through Eze after a horror error.
Roar defender Hosine Bility gave away possession with a sloppy header after a Phoenix goal kick. Eze pounced and sent a left footer into the back of the net as Roar goalkeeper Dean Bouzanis was left stranded by Bility.
Phoenix's 18-year-old goalkeeper Eamonn McCarron had a shocker the previous week in a 5-1 loss to Melbourne Victory but did well to save a Lucas Herrington header and a follow-up shot by Dimitri Valkanis.
McCarron was brave and brilliant throughout in a performance of real character to secure his side's first clean sheet of the season.
Tempers frayed when Armiento, against his former club, was sent off for raised studs that collected Roar defender Valkanis in the ankle. The foul led to a melee that involved a suite of players from both sides.
Roar striker Justin Vidic hit the woodwork after the break but the final pass continually let down the Roar.
Nagasawa and Retre stepped up for the Phoenix to secure a famous win.
Wellington central defender Manjrekar James was a tower of strength and had a blinder. Man of the match Eze was a constant threat.
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