The striker trod on Lowrys' foot as he made a tackle, but it wasn't deserving of a send off with a free-kick a more suitable punishment.
Glory's fourth win of the season put them three points behind the fourth-placed Melbourne City. Phoenix remain eighth, two points behind the sixth placed Western Sydney Wanderers.
Krishna scored thanks to a set up pass from Shane Smeltz and sloppy Perth defending from Alexander Grant.
His shot was initially saved by Liam Reddy but the Glory 'keeper couldn't stop it trickling over the line.
Phoenix continued opening up Glory on the counter attack and Kosta Barbarouses, Krishna and Smeltz all had good scoring chances. But a 30-plus metre bomb from Griffiths gave Perth a flattering 1-1 halftime scoreline.
They came out a different unit for the second half, Andy Keogh seemingly scoring in the 49th minute but getting called back for an incorrect offside call.
Two minutes later he delivered a cross that Taggart headed in and with the extra man advantage making life easier, the home side comfortably hung on for the win.
Phoenix coach Des Buckingham felt his team should have been further ahead in the first half and said the red card was undeserved.
"The send off looked very harsh and it looked like Roy had a heavy first touch, then withdrew his leg as he was about to make contact," Buckingham said.
"But we still need to be better in the second half regardless. The first half was very good but in the second half we need to be better in possession. The game should have been put to bed in the first half."
Meanwhile, Glory coach Kenny Lowe agreed Krishna was hard done by, but pleased for his team to get a win.
"It's always nice to win and they've worked ever so hard and they've been under the pump a little bit so I'm pleased for the players," Lowe said.
"I thought it (Krishna's red card) might have looked worse than it was after the event. His studs might have been showing, but I don't know if he followed through or if it was malicious.
"He's not that type of player. He's a typical forward who can't tackle. If I was sat in their shoes I'd be spitting feathers."
- AAP