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The abrasive halfback was introduced shortly after the Reds took a 19-13 lead 15 minutes into the second spell.
He put winger Scott Gregory over the line with a wonderful no-look back flip and a few minutes later dived over to get his name on the score sheet as well.
It was a huge win for the Highlanders in the circumstances.
They lost two players to the bin in the first half and had to operate with 13 men for about six minutes.
A combination of good defence and smart play limited the damage.
But Fakatava's introduction provided the attacking spark which has been missing for so much of the season.
The win has lifted the Highlanders into eighth place.
It looked bleak early, though. Lock Josh Dickson put his side under pressure when he was yellow-carded for a high shot in the 12th minute.
Dickson had just returned from a three-week ban for a similar offence. He actually had a week knocked off after undergoing remedial work on his tackle technique.
Rugged loose forward Marino Mikaele-Tu'u joined him on the sideline for a tip tackle four minutes later.
It was not very clever rugby from the visitors and the Reds cashed in.
Fullback Jock Campbell scored in the corner against the under-manned Highlanders.
Shortly after the Highlanders were restored to 15 players, Josh Flook climbed higher than Mitch Hunt to collect an up and under in the in-goal area and scored.
Powerful centre Thomas Umaga-Jensen shrugged off a couple of feeble efforts to reply for the Highlanders.
That good work looked to have been undone by James Lentjes, who had his pass picked off by Tate McDermott.
But the TMO found a little knock on and the try was ruled out.
Hunt slipped a late penalty inside the left upright to take his side into the break just 12-10 down.
The Reds went close early in the second spell when Jordan Petaia found space out on the left wing and put in a deft grubber. No 8 Harry Wilson scooped it up, but got hit a nice covering tackle and smashed into the ground hard.
He was stretchered off and replaced by Angus Scott-Young.
Billy Harmon made the try-saving tackle and had a big game.
The Highlanders edged ahead with a hard-earned penalty, but fell behind again when lock Ryan Smith smashed his way over after a lovely build-up where the Reds got some traction close to the ruck.
Earlier in the evening, the Blues hammered the Rebels 71-28 at Eden Park to consolidate their spot at the top of the competition standings.
They scored 11 tries, including a contender for the try of the year by Mark Telea, who leaped high to score in the corner with an acrobat effort.
Highlanders 27 (Thomas Umaga-Jensen, Scott Gregory, Folau Fakatava tries; Mitch Hunt con, pen 2, Marty Banks con 2)
Reds 19 (Jock Campbell, Josh Flook, Ryan Smith tries; Lawson Creighton con 2).