Groenewegen made his move 300 metres out from the line and held his advantage all the way after some fine work from Team BikeExchange into the final corners.
Jakobsen had been threatening at the front but the Quick-Step Alpha Vinyl star was unable to catch Groenewegen and add to his two stage victories.
Retaining GC superiority will be no small consolation for the 25-year-old, however, who hit the line ahead of Rudy Barbier (Israel-Premier Tech) in third and leads the Frenchman by 10 seconds overall.
The 177-kilometre stage would feature three categorised climbs and three intermediate sprints into Kazincbarcika, and Groenewegen was happy to make good on BikeExchange’s plan.
“The legs are really good all week, but the results were not there,” Groenewegen said.
“Today, we made a new plan. The team did an amazing effort for me. I’m really happy with my teammates that they could put me in a good position.
“Two hundred metres before the finish, I had very good legs for the sprint too.
“I was going and I saw nobody. The whole team was really strong. I’m really happy.”
The peloton never let the breakaway gain too much time in the fourth stage and eventually brought them back with 23 kilometres remaining.
By that point, Aaron van Poucke (Sport Vlaanderen-Baloise) had taken the KOM points for the red jersey, followed closely by Emil Dima (Giotti Victoria-Savini Due), Toon Vandebosch (Alpecin-Fenix) and Josu Etxeberria (Caja Rural-Seguros RGA).
As the final kilometres approached, it was BikeExchange in the best position to take the win with one more stage remaining.
“It’s a really important win,” Groenewegen added. “It’s been a difficult season, we had two wins with the sprint train already but after that we had a lot of sickness and I also crashed (here), but today we had a bit of luck.”
