Krishna's 89th-minute, near-post header from a cross from substitute Max Burgess was his second of the game and seventh of the season.
The win at ANZ Stadium lifted Phoenix to fifth above Adelaide, and ten points clear of eighth-placed Western Sydney.
It was hard luck for a Wanderers side that created just as many good chances in a free-flowing game, but lost two key overseas players to injury in the first half.
German playmaker Alexander Baumjohann limped off with a hamstring injury after five minutes and Spanish striker Oriol Riera came off with a groin problem just before halftime.
Prior to getting scan results on both men, Wanderers' coach Markus Babbel didn't expect either of them to be fit for Sunday's away game against Perth.
His Phoenix counterpart Mark Rudan praised his side for not dropping their heads after twice conceding the lead.
"We didn't play well today, we didn't hold on to the ball as well we could have and should have," Rudan said.
"We take a lot of pride in making sure we defend well from setpieces and we concede two from setpieces today so that's something I'm not very happy with.
"But in terms of everything else, I'm pretty pleased pretty content."
Phoenix opened the scoring with a well constructed and executed goal to Louis Fenton.
Wanderers equalised in the 42nd minute when captain and centre back Brendan Hamill headed in a well-delivered inswinging corner from substitute Nick Fitzgerald.
Phoenix hit the front again in the 82nd minute when goalkeeper Vedran Janjetovic raced out to clear a Cillian Sheridan through ball, but Krishna beat him to it and slid the ball inside the far post.
Keanu Baccus looked to have saved a point for Wanderers two minutes later, when he drilled home a shot from close range after a Fitzgerald corner went all the way to the back post.
A first-half penalty awarded when Bruce Kamau fell in the area after being challenged by Fenton was looked at by the VAR, which directed referee Jonathan Barreiro to look at a replay and he subsequently overturned his original decision.
"This is not the referee's fault today, it was our fault again, because we created many chances and we couldn't score enough goals," Babbel said.
"The (Phoenix) goals always come from nothing. I never had the feeling they were dangerous and then we do exactly what we said in the meeting before the game.
"Please be careful this is what they are looking for and we did exactly this."