Record Le Mans winner Kristensen increased his victory tally at La Sarthe to nine, yet surely none of his previous wins can match the poignancy of this latest success, which comes a day after fellow Dane Simonsen lost his life following a crash early in the race.
The result marks a third Le Mans triumph for Briton McNish while Frenchman Duval enjoyed his first taste of the victory in the endurance event at the fifth attempt.
The win was the fourth in succession for Audi, and their 12th in the last 14 years.
A record 11 safety car periods and a number of heavy downpours interrupted the flow of the 81st running of the annual endurance race.
Several hours of racing were lost to safety car periods, a fact borne out by the fact that the winners' total of 348 laps completed was well short of the 378 managed by the winners here 12 months ago.
The number eight car of Anthony Davidson, Sebastien Buemi and Stephane Sarrazin came second for Toyota, while the number three Audi of Oliver Jarvis, Marc Gene and Lucas di Grassi completed the podium.
Yet it was a slightly muted podium ceremony that played out before thousands of fans on the pit straight, with the events of yesterday very much in the forefront of the minds of the drivers and race organisers, who paid tribute to Simonsen before the winning national anthems.
GTE Am competitor Simonsen, 34, died when his Aston Martin came off the track through the Tetre Rouge corner and hit the barriers at high speed.
He was immediately attended to by doctors and transferred to the circuit medical centre where he died soon after due to his injuries.
A statement issued by race organisers said an investigation into the crash was focusing on the possibility that the accident occurred "due to circumstances in the race".
Onboard footage from the car following immediately behind Simonsen at the time of the crash appears to show another GT competitor further down the road going off the track in a separate incident just seconds earlier.
Simonsen's death inevitably diluted interest in the overall battle for victory, which nevertheless was as hard-fought as ever.
The number one Audi R18 e-tron quattro of Andre Lotterer, Benoit Treluyer and Marcel Fassler - winners here in 2011 and 2012 - had looked well set to make it a hat-trick as they pulled away into a commanding lead yesterday evening.
But the trio's hopes were extinguished as darkness fell when they lost 12 laps due to an alternator change. They recovered to take fifth place at the flag.
The number three Audi of Jarvis/Gene/Di Grassi was also in the wars, losing several laps when the R18 had to limp back to the pits after shedding a tyre, causing damage that necessitated a lengthy pit stop for repairs a short time later.
The dramas that hit the number one and number three cars played perfectly into the hands of Kristensen/McNish/Duval, who after a circumspect start to the race came through to claim a lead they would not relinquish.
A series of safety cars through the night punctuated the action at the front, with Sarrazin's hopes of closing in on the leading Audi hit when he was forced to queue in the pit lane for three minutes under one such caution.
Despite losing ground to Kristensen, Sarrazin's number eight car remained in the hunt and with just 23 minutes remaining the TS030 passed the Kristensen/McNish/Duval Audi before giving the place back to finish a lap down.
There was late drama for the sister Toyota, however, when Nicholas Lapierre lost control in a sharp downpour a little over an hour from the finish and crashed heavily into a tyre barrier on entry to the Porsche Curves.
The Frenchman initially clambered from the bruised TS030, but after a few minutes returned to the car - now missing its bodywork beyond the front tyres - and got it back to the pits before going on to claim a worthy fourth place.
Bertrand Baguette, Martin Plowman and Ricardo Gonzalez took the win in the LMP2 class for OAK Racing, GTE Pro honours went to Marc Lieb, Richard Lietz and Romain Dumas of Porsche, while the GTE Am win also went the way of Porsche thanks to Raymond Narac, Jean-Karl Vernay and Christophe Bourret.