Ably assisted by Test teammate Marnus Labuschagne (73), Khawaja scored 94 runs from 55 deliveries, shaking off a lukewarm run of BBL form and helping to hoist the Heat into another sudden-death clash with the Melbourne Renegades on Sunday.
Friday night's game ended a tumultuous season for the Thunder, who had defied a run of injuries and their historic thrashing from the Adelaide Strikers to qualify for the finals.
After the Heat posted the highest total for a BBL game at Sydney Showground Stadium (5-203), David Warner had the Sydneysiders off to a strong start (1-52) with his best knock of a lucrative BBL cameo.
But the Thunder were still eight runs behind the DLS par score when showers forced the covers on in the seventh over.
Play was set to resume 45 minutes later, with the Thunder requiring 38 runs from 13 balls in a condensed match, before more bad weather ended the match.
Khawaja's innings was his best in the BBL since the summer of 2015-16 and ensured he would finish the night as the tournament's highest run-scorer in finals - despite playing only eight innings in the post-season.
Khawaja and Labuschagne initially went at a steady clip after the early loss of Josh Brown (3) but the veteran cut loose with five boundaries from the first 10 balls he faced after drinks.
Grade cricketer and BBL debutant Ross Pawson was Khawaja's favourite target, copping five boundaries off his bat.
Spinner Usman Qadir (0-50) was also expensive as the Thunder struggled for a breakthrough in the absence of injured quicks Gurinder Sandhu and Brendan Doggett.
Ben Cutting finally dispatched Khawaja, who edged to Matthew Gilkes in the 17th over, just after Labuschagne brought up his maiden BBL half-century.
A swashbuckling cameo from Test revenant Matthew Renshaw (24 off eight balls) kept the Thunder on an even keel after the loss of Khawaja as the Heat set their rivals 204 for victory.
Warner (36 not out) looked more comfortable than in his five previous BBL innings this summer after the Thunder lost Matthew Gilkes (3) cheaply.
But Warner's effort was in vain as the rain thwarted the Thunder and brought his BBL summer to an end.
Warner's Test teammates Khawaja, Labuschagne and Renshaw are set to be available for selection against the Renegades, but spinner Mitch Swepson will miss out to prepare for the upcoming tour of India.
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