The Katusha rider emerged from the pack to win his first Tour stage, a yard ahead of Slovakian Peter Sagan, with French champion Arnaud Demare third.
The top of the general classification leaderboard remained unchanged.
Astana's Vincenzo Nibali retained the yellow jersey - two minutes, 23 seconds ahead of Team Sky's Richie Porte.
Thursday was a day on conserving energy for the riders looking to win the Tour de France, with two tough days in the Alpine mountains coming up this weekend.
"Sagan can only blame his legs which perhaps goes to show he has lost a little bit but take nothing away from Kristoff who finished that perfectly. "I think Sagan is missing a bit of top end. Had he ridden in a more conservative way earlier in the Tour he may have won a stage. He desperately wants one and he should be winning them. Today he did everything right but just didn't have the legs."
"The last two days have been anything but easy and suddenly it's got hot - it's just nice to get through these stages and into the mountains on Friday," said Australian Porte, who took over as Team Sky's race leader after Britain's defending champion Chris Froome crashed out on stage five.
"It's not an easy two days coming up. I think it's going to be absolutely crucial for the general classification so I'm looking forward to taking more time on the guys behind me."
There were four categorised climbs for the riders to negotiate on stage 12 but none were difficult enough to completely split the peloton, although a group of five riders were allowed to break clear early on and set up a lead of five minutes.
However, their advantage began to diminish after Team NetApp Endura's David de la Cruz suffered a front-wheel puncture as he took a right-hand corner and he took out Garmin-Sharp's Sebastian Langeveld.
Dutch champion Langeveld was fit to continue racing but De La Cruz was taken to hospital with a suspected broken collarbone.
The four out front became two on the category three 15.4km ascent of Col des Brosses when Florian Vachon and Gregory Rast dropped away and on the final category four climb Langeveld had no answer to a burst of speed from Australia's Simon Clarke with 26km remaining.
"We are definitely in for a General Classification battle. There will be no attacks on the descent from Palaquit because the final climb is so long - the last 30km of the stage is predominantly uphill. All the main contenders will be looking at each other on the final ascent and I don't think anyone will be saving anything."
Orica GreenEdge's Clarke was eventually caught on the descent into Saint Etienne by Cyril Gautier and Perrig Quemeneur, two Europcar riders who had raced clear of the peloton.
However, the peloton timed their chase to perfection, catching the escapees with 5km remaining.
Omega Pharma - Quick-Step's lead-out train looked well set to deliver Matteo Trentin to the line for a second stage win on this year's Tour but it was Kristoff who emerged from their slipstream to take the win.
"I have been dreaming about this since I was a small child and to finally achieve it is nice," said Kristoff. "There will be champagne but Friday is a hard stage so there cannot be too much party."
Cannondale's Sagan, who is yet to win a Tour stage in 2014, finished second for the fourth time - he has eight top-five finishes from 12 stages - to extend his lead in the green points jersey standings to 150 over Bryan Coquard of Europcar.
Stage 12 took the race past the famous vineyards of the Loire Valley 
Race leader Vincenzo Nibali (in yellow jersey) rides in the slipstream of his Astana team-mates Stage 12 result
1. Alexander Kristoff (Nor/Katusha) 4hrs 32mins 11secs
2. Peter Sagan (Svk/Cannondale) same time
3. Arnaud Demare (Fra/FDJ.fr)
4. Michael Albasini (Sui/Orica)
5. Ramunas Navardauskas (Ltu/Garmin)
6. Matteo Trentin (Ita/Omega Pharma - Quick-Step)
7. Daniele Bennati (Ita/Tinkoff - Saxo)
8. Bryan Coquard (Fra/Europcar)
9. Daniel Oss (Ita/BMC Racing)
10. Samuel Dumoulin (Fra/AG2R)
General classification after stage 12
1. Vincenzo Nibali (Ita/Astana) 51hrs 31mins 34secs
2. Richie Porte (Aus/Team Sky) +2mins 23secs
3. Alejandro Valverde (Spa/Movistar) +2mins 47secs
4. Romain Bardet (Fra/AG2R) +3mins 01secs
5. Thibaut Pinot (Fra/FDJ.fr) +3mins 47secs
6. Tejay van Garderen (US/BMC Racing) +3mins 56secs
7. Jean-Christophe Peraud (Fra/AG2R) +3mins 57secs
8. Bauke Mollema (Ned/Belkin) +4mins 08secs
9. Jurgen Van den Broeck (Bel/Lotto) +4mins 18secs
10. Jakob Fuglsang (Den/Astana) +4mins 31secs
Selected others
12. Geraint Thomas (GB/Team Sky) +5mins 17secs
111. Simon Yates (GB/Orica Greenedge) +1hr 33mins 5secs
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