The German giants won 5-1 on Tuesday night to send them into the top eight of the table, with Olise the star of the show.
Shakhtar took a shock lead through Kevin on five minutes but Bayern hit back shortly after courtesy of Konrad Laimer.
He was assisted by Olise, who scored his side's third goal of the night from the penalty spot to put the result out of reach.
However, he saved his best efforts to last by scoring an incredible solo goal during stoppage-time at the VELTINS-Arena.
Olise collected the ball around halfway into Shakhtar's half, turned his back towards goal and ran past two opposition players.
MORE ON THE CHAMPIONS LEAGUE
Villa inflict unwanted piece of history against RB Leipzig with huge Champions League win
Mbappe only bettered by Messi as he hits Champions League milestone before injury
The Frenchman kept sprinting, evading more defenders en route to the penalty area, before deceiving the goalkeeper and slotting in.
With two goals and an assist, Olise is the youngest ever player to be directly involved in three goals in a single Champions League match for Bayern.
He has done so at the age of 22 years and 364 days, with the winger celebrating his 23rd birthday on Thursday.
Olise has now scored nine goals and assisted another seven across all competitions for Bayern in 21 appearances.
Most read in Champions League
'How professional are you today?' - Bellingham ribs Richards in wholesome interview
EA FC 25 RTTK upgrade tracker: How it works and dates explained for Road to the Knockouts
Villa inflict unwanted piece of history against RB Leipzig with huge Champions League win
Mbappe only bettered by Messi as he hits Champions League milestone before injury
It's seen him continue his excellent start to life at the Bundesliga outfit since his near £51million summer move from Crystal Palace.
Olise has started in all but one of their Champions League matches this season, with Bayern recovering from a shaky start.
Despite thrashing Dinamo Zagreb 9-2 in their opening match of the league phase, they were beaten by Aston Villa and Barcelona.
They were left lingering above the bottom 12 as a result but have since turned their fortunes around.
Vincent Kompany's side beat Benfica and Paris Saint-Germain by 1-0 scorelines before Tuesday night's win at Shakhtar.
Feyenoord and Slovan Bratislava are their final two opponents ahead of the last 16, with both matches coming in the New Year.