Houghton's outstanding set shot from an angle was the first time the Power had led all game and they held on for their sixth-straight win, beating the gallant Giants 7.1 (43) to 6.6 (42).
It means instead of finishing eighth and heading to Perth next weekend to play Fremantle in an elimination final, Port take sixth spot and host Richmond.
Power coach Lauren Arnell noted Sunday's boisterous home crowd of more than 4000 at Alberton Oval was the "top end of the tree" for an AFLW attendance and her players used their fans' energy in the last term.
But Port got out of jail and Arnell also said it was an important lesson ahead of the finals.
"It's for our fans and our people ... you could absolutely see the way our group fed off our supporters today," she said of securing the home elimination final.
"It (the near-miss) is a nice little kick in the backside."
Abbey Dowrick (soreness) and Matilda Scholz (calf) were crucial late withdrawals for Port, but Arnell is confident they will be back next weekend.
While it meant the Giants ended their season with an eighth-straight loss, they were mighty.
"The level they got to in their game suggests very strongly that the ladder tells a bit of a lie about the team they are," Arnell said.
The heartbreaker left Giants coach Cam Bernasconi with mixed emotions.
"It's a pretty brutal way to finish your game. I'm so proud with how the group came and fought so hard," he said.
"To lose like that, it rips your heart out. I feel for the group right now."
He said the Giants were motivated to do well for Alicia Eva, playing her 75th game, and Indi Linde, who made her AFLW debut.
After returning from an ACL rupture, Giants player Meghan Gaffney suffered a knee injury in the third term and Bernasconi said his fingers were crossed for her.
The experience of Power veteran Kirsty Lamb was critical when the match was on the line.
Lamb snapped the opening goal of the final term then won a free kick with less than two minutes left.
Her long pass found Houghton, who marked and kicked the match winner.
The Giants have averaged 70 tackles per game, but on Sunday they had a whopping 106 to 80.
GWS captain Bec Beeson was superb, kicking their only goal in the last term and amassing a game-high 25 disposals in her best-afield performance.
She stayed on the ground in the frenetic last quarter despite a head knock.
Port's Maria Moloney was critical with her 17 disposals, including 13 contested possessions.
GWS held a game-high lead of 17 points in the third term, but Port kept with them and kicked three goals to one in the last quarter.
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