Warner's 82 steered the Thunder to 6-180 at the Gabba on Saturday, before fellow 39-year-old and retired Test great Usman Khawaja stroked 78 to steer the Heat home with 22 deliveries remaining.
Warner was unable to field after being hit flush on his left knee, which was unprotected as he crouched low while attempting to sweep Xavier Bartlett.
Chris Green captained in Warner's absence throughout Brisbane's innings.
Heat skipper Khawaja, who signed off as a Test player two days ago, switched effortlessly to white-ball mode, sharing in a 93-run third-wicket stand with Matt Renshaw (42no).
When Khawaja succumbed with the finish line in sight, he received a standing ovation from the Brisbane crowd, as much for his fine innings as his entire 88-Test journey.
Khawaja officially retired from Test cricket after Australia clinched the Ashes series 4-1 with victory at the SCG on Thursday.
The popular veteran admitted he was overcome with emotion in the lead-up to and during his final Test innings.
"I was trying to act cool, but this whole Test I've struggled to contain my emotions," Khawaja said after Thursday's victory.
"I found it really hard to concentrate, really hard to get into rhythm."
There were no signs of nerves at the Gabba on Saturday, with Khawaja helping himself to seven fours and three sixes in his 48-ball masterclass.
Khawaja was playing his 72nd BBL match, and he has shown a real liking for the format, having scored two centuries and 14 half-centuries at a strike-rate of more than 130.
Earlier Jack Wildermuth laid a raucous foundation, taking Wes Agar down for three sixes and a four in the third over.
Wildermuth's whirlwind cameo ended on 39 off 15 balls, thanks to a superb diving outfield catch from Tanveer Sangha.
Agar's nightmare continued when he dropped a sitter to reprieve Nathan McSweeney first ball.
It didn't prove too costly, McSweeney sweeping Chris Green down David Willey's throat for 12.
Earlier, Warner continued his purple patch after starting the New Year with an unbeaten 130 and 67 not out.
He looked on track for another ton before falling in calamitous fashion, soon after copping the blow to his knee.
Sam Billings (34) top-edged a sweep off Renshaw to deep midwicket, where Marnus Labuschagne uncharacteristically grassed a regulation chance.
But nearby McSweeney pounced on the ball and threw a bullet to wicketkeeper Jimmy Peirson.
Warner wanted a second run before being caught well short after being sent back by Billings, who appeared to be ball-watching, seemingly not expecting Labuschagne to drop the catch.
Renshaw (2-29 off four overs) was the pick of the Heat attack with his part-time finger spin.
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