Quintana, 24, completed the 26.8km ascent of Monte Grappa in a blistering time of 1hr 5.37min to take his second stage win of the race by 17 seconds over the impressive Fabio Aru (Astana).
Colombia's Rigoberto Uran (Omega Pharma-Quick Step) set the third quickest time, 1:26 down on his compatriot, and now trails Quintana by 3:07 in the general classification with two stages remaining.
After an extraordinary ride up the mist-clad Alpine ascent, 23-year-old Aru moved into the third podium position and trails Uran by just 41 seconds ahead of Saturday's stage 20 to Monte Zoncolan.
Quintana could set only the sixth best time at the first check after the flat 7.5km ride to the foot of the climb, the race leader decked out entirely in pink riding 38 seconds in arrears of Germany's Patrick Gretsch (Ag2R-La Mondiale).
But this time trial was always going to be decided on the precipitous slopes of Monte Grappa, with its maximum ramps of 14% coming near the summit where thousands of fans had congregated to cheer on their heroes.
Like all the GC favourites, Quintana switched from his time trial bike at the foot of the climb - but unlike his rivals, the pint-sized climber also swapped his aerodynamic helmet with a normal version that was a lighter shade of pink.
But it was Aru, wearing the white jersey for the best young riders by default, who set the target time at the second check 7km from the finish and just ahead of the steepest section of the climb.
At this point, Australian veteran Cadel Evans (BMC) was already two minutes down while 2012 champion Ryder Hesjedal (Garmin-Sharp) was 2:30 in arrears after being forced to change his bike for a second time owing to a mechanical.
A flurry of excitement occurred when Domenico Pozzovivo (Ag2R-La Mondiale) caught Canada's Hesjedal - who started a full three minutes before the Italian - and then Aru in turn passed the young Pole Rafal Majka (Tinkoff-Saxo), who started the day level on time with Aru.
Time projections had Aru leading Quintana by six seconds - and when Aru burst over the finish line more than two minutes ahead of his nearest rival, Pozzovivo, it looked like the winner atop Monte Campione last weekend would be crowned once again on Monte Grappa.
But Quintana fought back to put in a huge 23-second swing over the final 2km to deny the home fans something to celebrate - and in turn take his second win of the race.
France's Pierre Rolland (Europcar) was fourth on the day, 1:57 down on Quintana, while Pozzovivo had to settle for fifth, at 2:24. Franco Pellizotti (Androni), Majka, Sebastian Henao (Sky), Tim Wellens (Lotto Belisol) and Dario Cataldo (Sky) completed the top ten, with Cataldo finishing 4:10 down on the indomitable Quintana.
Rolland drops off the podium to fourth place on GC, 5:26 down on Quintana, and ahead of Pozzovivo and Majka. Despite losing time to the main GC favourites, Evans rose from ninth to seventh but is now 9:25 off the summit.
The top ten on GC is completed by Dutch youngster Wilco Kelderman (Belkin), Hesjedal and Robert Kiserlovski, the Croatian rider from Trek a huge 13:59 down on the maglia rosa.
BIG WINNER OF THE DAY: Quintana and Aru aside, it was a highly memorable day for Belkin's Josh van Emden: the Dutchman may have finished almost 12 minutes down in 120th place but he did stop to propose to his girlfriend half way up the climb and so will feel every bit the winner - provided she did say yes...
BIG LOSER OF THE DAY: He may have finished third, but Rigoberto Uran's chances of winning the Giro now seem fairly remote - and the Colombian will be looking over his shoulder at third-place Fabio Aru on Monte Zoncolan.
KEY MOMENT: Those final two kilometres from Quintana were quite something - and had he failed to win today then some of the wounds relating to the Stelvio neutralisation fiasco may have reopened. Taking the victory in such pulsating fashion should now put the events of the Stelvio to bed.
TALKING POINT: Just how good is Fabio Aru? Astana team-mate Vincenzo Nibali - the defending champion - may not be here, but the Italian tifosi have a true talent to cheer in the Sardinian.
COMING UP: The final day in the mountains is the 167km stage 20 from Maniago to Monte Zoncolan which features three hefty climbs in the last third, including the summit finish up the infamous Zoncolan. The fight for the pink jersey may well be done and dusted but those remaining two podium places have yet to be decided.
- Sports & Recreation
- Monte Grappa
- Rigoberto Uran
- Fabio Aru
- Monte Zoncolan
- Domenico Pozzovivo