The Queensland and Australia centre had been dropped to the bench after the round-two loss to Parramatta and did not get on the field in last week's clash with Melbourne.
The 27-year-old came on in the first half against the Dolphins at Suncorp Stadium on Friday night after the Broncos lost winger Grant Anderson to a suspected medial collateral ligament (MCL) injury.
He defended resolutely and was desperate in his chase of Reece Walsh's 72nd minute bomb that the Dolphins let bounce. Shibasaki swooped to score and seal Brisbane's sixth win out of seven clashes with their fierce rivals.
Brisbane captain Adam Reynolds, returning from a rib injury, was magnificent with his kicking game on song, while Broncos centre Kotoni Staggs scored a double amid another big game against the Dolphins.
The Broncos had a turbulent week after defensive coach Ben Te'o resigned but they showed great defensive clout to repel the Dolphins.
"The boys had to dig pretty deep because they were coming hard and fast," Broncos coach Michael Maguire said.
"But I know what's inside the group. I was happy with the resilience."
The Broncos led 10-6 at halftime with both sides going close to scoring on several occasions in an end-to-end display of expansive rugby league.
Staggs, who now has six tries in seven matches against the Dolphins, opened the scoring when he grounded a silky Ezra Mam grubber kick.
The Dolphins had tries disallowed to five-eighth Kodi Nikorima and second-rower Kulikefu Finefeuiaki for obstruction and a forward pass, respectively.
"It was a tough game," Dolphins coach Kristian Woolf said.
"When we got our opportunities, we didn't nail them."
The derby threatened to erupt when Dolphins co-captain Tom Gilbert was ruled to have hit Walsh late and Broncos lock Pat Carrigan took exception.
From the resulting penalty Reynolds turned on the magic when he fooled the Dolphins defence with a crafty short grubber that he collected himself and darted over to score.
The Dolphins hit back when fullback Hamiso Tabuai-Fidow found a gorgeous cutout ball to winger Jamayne Isaako who converted his own try from the sideline.
An incredible reverse flick pass on the last tackle by Broncos prop Ben Talty put Walsh over straight after halftime.
Reynolds was key in the build-up after another crafty grubber trapped the Dolphins in their own in-goal.
The Broncos repelled several attacking raids before Mam served up a try on a platter for Dolphins centre Jake Averillo with a terrible pass that went behind Walsh.
The kick-chase and clean-up work of Broncos second-rower Jordan Riki was a highlight as was the dynamic running of his Dolphins counterpart Finefeuiaki.
Carrigan was the Battle Medal winner as man of the match.
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