Later on Saturday, Canberra United won 2-1 at Perth Glory to leap into sixth and stay in the finals hunt.
The Victory (44 points) remain firmly in the hunt for the ALW premiership after drawing within two points of leaders Melbourne City (46) and five clear of Adelaide (39).
City, who face Wellington on Sunday, and the Victory each have three games left to play, while the Reds have two.
The top two get the first week of finals off, then host the second match of their two-legged semi-final.
Adelaide entered Saturday's game three points behind their hosts and needing a win to realistically stay in the hunt for the premiership plate.
Already without strker Erin Healy (quad), Adelaide suffered a blow before the game even started when goalkeeper Claudia Jenkins suffered a knee injury in the warm-up, with 16-year-old Ilona Melegh debuting as a late replacement.
Coach Adrian Stenta was confident Jenkins' injury wasn't serious.
The Pride Cup clash at AAMI Park shaped as the game of the round, but threatened to fizzle out to a 0-0 draw for much of the afternoon.
Then Jessica Young worked the ball out wide to Flannery, who cut onto her right and let rip from the edge of the box in the 69th minute.
United earned the chance to equalise when Emily Gielnik needlessly handballed in the penalty box, with Holmes coolly converting the spot kick in the 85th minute.
But five minutes later, Gielnik, overlooked for April's Matildas squad, made amends when she burst down the right in added time and lifted a cross into a dangerous area for Flannery to thump home a header.
"She works so hard for the team. A lot of work that she does goes unseen, that unselfish running and tackling," coach Jeff Hopkins said of Flannery.
"But we brought her here to score goals and and to create things as well."
At the Sam Kerr Football Centre, Perth defender Natalie Tathem was substituted off with a right knee injury in the 15th minute, and will hope she has not suffered a dreaded ACL tear.
A minute later, Mary Stanic-Floody worked the ball to Michelle Heyman and the veteran striker burst forward to open the scoring.
Stanic-Floody doubled Canberra's lead from the penalty spot in the 21st minute.
Canberra's Bethany Gordon smacked a penalty over the bar in the 51st minute and nine minutes later, Perth's Tijan McKenna scored to bring the game to life.
But Canberra (27 points) held on to leap into the top six, while 10th-placed Perth sit five points back with two games to play.
