Defying heavy rain, Astana's Nibali was the only rider in the peloton to complete the demanding race against the clock in less than 45 minutes as he moved closer to a first Giro d'Italia crown.
Despite rolling down the start ramp in the Velodrome of Mori a full three minutes behind BMC's Evans, Nibali finished just moments after the Australian veteran. Punching the air with his fist, Nibali crossed the line in Polsa to set a blistering time of 44mins and 29secs - a full 58 seconds ahead of the target time set by Spaniard Samuel Sanchez of Euskaltel.
Nibali's belated first stage victory in a race that he has largely dominated since the opening week saw the 28-year-old increase his lead to 4:02 over Evans on GC, with Colombian Rigoberto Uran (Team Sky) a further ten seconds back in third place.
With just two mountain stages remaining ahead of the final processional ride into Brescia on Sunday, the Sicilian looks all but certain to add the Giro to his extensive palmares, which also includes the 2010 Vuelta a Espana crown.
Trailing the race leader by 1:26 in the overnight standings, 36-year-old Evans was expected to vie with Nibali for the stage victory on Thursday. Although he may have been dreaming of the pink jersey, Evans would have known that anything higher than 12th place would have put him back into the top of the red jersey points standings at the expense of Briton Mark Cavendish (Omega Pharma-Quick Step).
But with rain starting to fall soon after the final riders rolled down the start ramp, Evans - just hours after being promised the BMC leadership over Tejay van Garderen in next month's Tour de France - struggled to make an impact en route to finishing in 25th place, 2:36 down on the impressive Nibali.
Michele Scarponi (Lampre-Merida) had ridden the first half of the climb with gusto to beat Sanchez's time at the 9.5km split by seven seconds before Nibali showed his strength by shaving 31 seconds off his compatriot's effort.
Scarponi, the 2011 winner, slowed on the second steeper section of the time trial to post the fourth best time, 1:21 down on Nibali and one second slower than third-place Damiano Caruso (Cannondale).
Uran struggled to get into a decent rhythm in the initial climb, setting only the 17th best time at the split at Brentonico. But the Colombian recovered on the harder slopes towards the finish and posted the sixth best time, 1:26 seconds down on the winner.
The Team Sky leader stays in third place on GC but moves within 10 seconds of Evans - but will have to defend his place on the podium from the threat of Scarponi, who lies just over a minute behind in fourth place.
Scarponi's Lampre team-mate Przemyslaw Niemiec of Poland is fifth at 6:09 after a solid if spectacular ride.
If the battle for the pink jersey now looks all but over, then the ultimate destination of the white jersey remains very much gloriously unknown after Colombian Carlos Betancur (Ag2R-La Mondiale) and Poland's Rafal Majka (Saxo Bank-Tinkoff) continued their enthralling duel during the gripping ITT.
Separated by just five seconds on GC going into the test, the pair swapped places - and jerseys - at the end of the day when Majka managed to take back seven seconds after digging seep in the second phase of the race.
The Polish youngster rises to sixth place on GC, two seconds ahead of Betancur, after Italy's Mauro Santambrogio (Vini Fantini) could only post the 24th best time. Stage 14 winner Santambrogio is now eighth on GC, 7:30 down on Nibali.
After his second-place ride Sanchez moves into the top ten behind stage 16 winner Benat Intxausti at the expense of Dutchman Robert Gesink (Blanco), who disappointed in 29th place.
With Nibali sitting pretty in pink with more than four minutes to play with, the race now enters its final decisive phase with two back-to-back stages in the high mountains.
Friday's 139km stage 19 was due to feature the gruelling climbs of the Gavia and Stelvio ahead of a summit finish in Val Martello - but heavy snow and sub-zero temperatures have forced the race organisers to change the route at the 11th hour.
The amended stage will still start in Ponte di Legno but the revised 160km route will feature the Passo Tonale and Passo Castrin climbs ahead of the Cat.1 summit finish at Val Martello Martelltal.
Saturday's stage 20 - which includes the unforgiving Passo di Giau and a summit finish on Tre Cime di Lavaredo - could also be rescheduled due to the weather.