The Heat keeper smashed 14 fours and a six in her stunning 102 off 55 balls before Laura Harris hit the winning boundary with three deliveries left as the Heat chased down the Thunder's impressive 7-171 at Cazaly's Stadium and jumped to second spot on the ladder.
Grace Harris's quickfire 13 at the top and a pair of 15s to captain Kirby Short and Jess Jonassen were the closest anyone got to the dominant Mooney, who was the difference between the two sides.
But when Mooney, who had gone 12 innings without a half century since hitting 63 not out in the Heat's season opener, was stumped off Harmanpreet Kaur (2-23) in the 17th over, the Thunder suddenly looked to have the upper hand.
But a poor 19th over from Kaur which went for 13, including a no-ball, meant the Heat required six off the last over and Harris didn't hold back driving Nicola Carey down the ground to raise victory.
The win was watched by 4,673 vocal fans at Cazaly's Stadium in Cairns, the second weekend in a row the Heat has enjoyed support in Regional Queensland after last Saturday's record breaking night in Mackay.