Perth were seven points clear on top of the table when they beat Victory 2-1 on January 2.
But an eight-match winless run has left them in a five-team battle to secure a top-two berth.
Krishna now has nine goals for the season, putting him just four behind Sydney's Marc Janko in the race for the golden boot.
His input was all the more important after star striker Nathan Burns was ruled out of Saturday's match with a hip injury.
Glory controlled most of the opening half but they also produced a host of defensive mistakes to give Wellington some meaningful sniffs.
Krishna almost scored in the third minute when he picked off Jamieson's back pass before being blocked by Vukovic.
And the Glory were made to pay for their sloppiness when Krishna charged at Risdon and got the defender's clearance to rebound off his foot and in for a goal.
Zadkovich, who replaced the suspended Mitch Nichols in the starting line-up, brought the 9178 crowd to life with his unexpected thunderbolt.
Glory looked the most likely to produce the winner in the second half and Andy Keogh came close in the 77th minute when he skipped past two defenders before his shot was saved.
But just one minute later Wellington had the lead, with Krishna patiently assessing his options before outmanoeuvring Jamieson to score the winner.
"A few of the boys have nose bleeds. They're not used to it," Phoenix coach Ernie Merrick said of his team's rise to the top.
"It's a good feeling. It makes the flight back a bit easier. It's not an easy place to come and win."
Glory coach Kenny Lowe rued his side's costly errors.
"At the end of the day, you can't give two goals away like we did, especially when you're top of the table," Lowe said.
"When you play good sides, if you make errors, you generally get hurt. And we got hurt by two poor errors.
"You can't make those mistakes and expect to come out with something."
- AAP
