The first half featured little open play as both sides became locked in a physical battle in the middle of the park, with late hits and niggling tactics a constant feature of every gang tackle.
Queensland adjusted better to the grinding nature of the contest, while their senior playmakers Cameron Smith and Thurston directed play efficiently to ease the early pressure on halfback Daly Cherry-Evans' injured right knee.
Tensions threatened to boil over on several occasions but a penalty against New South Wales for slowing the play the ball allowed Thurston to post first points with a kick from close range in the 14th minute.
The Blues battled to improve their field position but lost a chance to level when a rush of blood from five-eighth Josh Reynolds saw him take a quick-tap instead of allowing Hodkinson a relatively easy shot at goal.
Any rising momentum from the home side was quickly quelled, however, when prop James Tamou was penalised for a forearm on Nate Myles, gifting Thurston his second goal to see him overtake Meninga's record as the highest point-scorer in Origin history.
Both sides had attacking chances inside the closing stages of the first half but a lack of structure from the Blues saw them come up empty, while the Maroons went to the sheds with their tails up.
A dangerous lifting tackle from Anthony Watmough in the first minute of the second-half allowed Queensland to head straight back down into opposition territory, and the heavy defensive load looked to be taking its toll on the Blues.
They clung on and were fortunate not to fall further behind when fullback Jarryd Hayne arrived to knock the ball from a rampaging Sam Thaiday's grasp as he dived for the line.
Hayne, New South Wales' best player in game one, was kept quiet by the Maroons defence, and struggled to get the ball with any space or time.
Three attacking sets passed without him touching the ball and the Blues attack suffered as a result. It took an age for their playmakers to take charge but the Maroons' line finally yielded when Hodkinson produced the match-winning play.
The final stages were again marred in controversy with Reynolds and Thurston being placed on report but the Blues cared little as they set about celebrating their first series success since 2006.
New South Wales 6 (Hodkinson try; 1 con)
Queensland 4 (Thurston 2 pens)