Bergsma clocked 12 minutes, 44.45 seconds for his 25 laps, smashing the previous mark by a huge 14 seconds and ending only three seconds shy of Kramer's world record set seven years ago on the high-altitude oval in Salt Lake City.
Pre-race favourite Kramer cited "too many small injuries" after claiming silver, 4.57 seconds off Bergsma's time, with compatriot Bob de Jong almost 23 seconds back from the winner.
South Korean defending champion Lee Seung-hoon was a distant fourth after starting fast alongside Kramer but fading badly.
The Dutch took their speed skating medal haul to 19 out of a possible 27 with their fourth sweep of the podium and fifth win from nine races in a show of dominance not seen before at a Winter Olympics. The three Olympic medals pushed them to 101 in the sport's all-time list.
Bergsma, who took bronze in the 5,000m on the opening day of competition, was blown away by his upset victory.
"It is a fantastic feeling, I knew with my current shape I could do it, but these are the Olympic Games," he told reporters after taking a congratulatory call from Dutch Prime Minister Mark Rutte.
"I knew with a good race I would win here. I watched Sven, he held on for a very long time, but finally he broke."
Kramer beat Bergsma to win the 5,000m gold but he spent little time enjoying victory as attention quickly switched to seeking retribution in the marathon speed skating race.
Four years ago in Vancouver, Kramer was celebrating what he thought was 10,000m victory only to find himself disqualified for an incorrect lane change after wrong advice from his coach. This was meant to be a chance to right the wrongs, but Bergsma had not read the script.
Having won the only 10,000m World Cup race in December by 12 seconds, Kramer entered the oval in confident mood, smiling and waving to fans with his expected victory bid aided by a number of withdrawals from the longest discipline.
That positive glow was quickly wiped out by the 28-year-old Bergsma who set a blistering pace in the penultimate heat to set a tough task for the poster boy of Dutch speed skating.
Kramer, starting in the final heat alongside South Korean Lee, reacted to the scorching time by flying out of the traps to clock several quick splits to leave him on world record pace with 10 laps to go.
But fatigue eventually kicked in on the marathon skate and he fell firstly outside of the world record time and then crucially behind Bergsma's splits with three laps remaining.
"I set off on a really fast time, tried to beat him and first couple of laps I was skating too fast and I blew up," Kramer told reporters.
"I'm really disappointed with the race today but Jorrit did an amazing job, I couldn't beat him, he set a world record for sea level, it was a pretty fast time. I knew before the race it was possible but I had too many problems with my back."
Kramer's collapse meant Bergsma could embrace his coach and celebrate victory while Kramer still had a lap to go, safe in the knowledge his time on the Adler Arena ice was too hot.
Kramer shook the hand of the victor but was despondent looking on the podium and greeting the many Dutch fans in attendance.
Bergsma, however, was unconcerned. "Yeah of course it was a real pity what happened in Vancouver and I can understand people really wanted to see Sven win here for revenge but I'm skating here for myself," he said.
"My goal was to win gold over here and I'm not giving the gold away for Sven's story."