Adelaide posted 7-159, largely due to a late flurry from top-scorer Alex Ross (47 from 38 balls), Michael Neser (27 from 16) and Adil Rashid, who made 14 from just three balls.
Rashid smacked a four, four and six from the last three deliveries of the innings to blow out Clint McKay's bowling figures to 3-44.
Khawaja then blazed a half-century from just 24 deliveries - from his first 21 balls, he smacked nine fours and six.
He then motored to his ton from only 55 balls in an innings which sucked the spirit from the Strikers and their parochial 48,699-strong home crowd.
Khawaja's onslaught ensured the Thunder were well ahead of the curve - after five overs, they were 1-57; after 10, they were 2-91.
From there, they cruised to victory with Khawaja fittingly reaching his century, from just 55 balls, with a six - he struck 13 fours and three sixes all up.
Despite the emphatic win, the Thunder will be the away team in Sunday's title decider.
The winner of the Stars' clash with the Scorchers, who are seeking a third crown in a row, will host the final as they finished higher on the ladder than the fourth-placed Thunder.
Khawaja's heroics follow a breakout Test summer for Australia and propel him into considerations for the looming T20 World Cup.
"I'm hitting the ball really well," Khawaja told Network Ten.
"I don't think too much when I play cricket.
"I wanted to get off to a good start and thankfully I did ... and I'm glad I was there at the end."
- AAP
