A frantic final two minutes saw Yasmin Clydsdale have the ball kicked from her grasp while attempting to ground the ball, with Jesse Southwell's conversion edging NSW into a 18-14 lead.
The Blues got a penalty from the first tackle off the kick-off but couldn't score on a Hail Mary play with the siren sounding.
NSW were victorious in front of a record 18,275 crowd but Queensland were crowned the series champions after winning game one 18-10.
The Blues needed to win in Townsville by eight or more points to retain the shield on aggregate but came up just short.
"It does feel a bit mixed," Queensland coach Tahnee Morris said.
"The girls are celebrating but it is a weird feeling.
"It just goes to show you know the points aggregate came into play and we scored more points and that's how we won the series."
All three of Queensland's tries came in the opening half and they spent the back-end of the contest scrapping for every metre, defending wave after wave of a Blues onslaught.
"I was really impressed with the way we stuck to our game plan and our structures," NSW coach Kylie Hilder said.
"A couple of lapses but really proud of the girls (and) the way they fought back to get that win."
Trailing 14-6 to begin the second half, NSW started just like they did in the first with a quick try to Tiana Penitani.
A beautiful shortside hands play put the powerful winger over and Southwell narrowed the deficit to two with a penalty a short time later.
Queensland then found themselves under sustained pressure till the very end, with their important away win in Sydney the difference.
Fullback Tamika Upton's cover defence was outstanding, as was her ability to read the Blues' attack and thwart kicks behind the line.
Tazmin Gray had a blinder in the middle and was awarded both player of the match and series.
Simaima Taufa was enormous for NSW in her return from injury, as was Emma Tonegato who ran for a game-high 207 metres as four of the Blues' back five finished with 100 or more.
Penitani opened the scoring after four minutes and NSW raced out to a 6-0 lead when Southwell slotted a penalty goal.
The visitors showed their hand early, eager to throw the ball around and attack both edges, but against the run of play Gray ran a tight line off Tarryn Aiken's shoulder before offloading to Upton for Queensland's opening try.
From an error then penalty in NSW's half, the Maroons were in again when Gray somehow managed an offload off the ground, as did Evania Pelite right after for Emily Bass to score.
Aiken then showed her skill from the restart to beat her defender and fend off Tonegato for Queensland's third as the Maroons went bang-bang.
That would be Queensland's final score of the night, but they did enough to hoist the shield in front of home fans.
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