NSW had scored the only two tries of the game up until that point and looked set for a hard-fought victory with several of their stars sidelined with injury.
Queensland five-eighth Mike Harris booted six penalty goals from as many attempts as well as the final conversion and his faultless kicking performance proved the difference.
New Zealander Harris certainly didn't have the spark of the man he's deputising for at No.10, Quade Cooper, but his nerve under pressure saw the Reds succeed in their first baby step towards a title defence.
Despite Wycliff Palu's first-half try, NSW trailed 15-14 with thirteen minutes left on the clock before crafty No.9 Pretorius darted from close range and reached out to touch down to give the Waratahs a 21-15 lead.
Harris cut that back with a penalty shot shortly after and then Pretorius was replaced - bringing McKibbin into the action.
Daniel Halangahu's selection as NSW captain was questioned during the week but the 27-year-old led from the front with some incisive second-half runs and a good clearing kicking game - but ultimately was left devastated at the death.
Wallabies stars Berrick Barnes, Drew Mitchell, Lachie Turner and Rocky Elsom were among the throng of injured Waratahs watching from the stands, but the home side overcame poor discipline to capitalise better than their opponents.
However in the end it wasn't enough and the pain of this defeat won't wash away easily.
QUEENSLAND REDS 25 (Dom Shipperley try Michael Harris con 6 pens) bt NSW WARATAHS 21 (Wycliff Palu, Sarel Pretorius tries Daniel Halangahu con 3 pens) at ANZ Stadium. Referee: Jaco Peyper. Crowd: 32,071.