Overnight leader Tadej Pogacar retains the yellow jersey by 45sec from Belgian Remco Evenepoel while defending champion Jonas Vingegaard is third.
Rounding out the top five are Spaniard Juan Ayuso and Pogacar's Slovenian compatriot Primoz Roglic.
Jasper Philipsen was second in Dijon after being well set up by Mathieu van der Poel while green sprinters' jersey wearer Biniam Girmay was third.
The two previous sprints on the Tour were record breakers with the 39-year-old Mark Cavendish winning his 35th career stage on the Grand Boucle on Wednesday.
On stage three Eritrean Girmay became the first black African to win a stage on the race.
In 2020, Groenewegen, 31, was banned for nine months for his role in a near-fatal crash that sent Fabio Jakobsen over a safety barrier and into a metal post at the Tour of Poland.
Jayco-AlUla's Groenewegen claimed his sixth Tour victory less than three weeks after winning the Dutch national road race title.
Intermittent showers with temperatures of around 20 degrees Celsius (68 degrees Fahrenheit) spared the extreme heat of the opening days but Vingegaard's team Visma frequently upped the tempo when the roads narrowed, causing stressful gaps in the peloton.
There was also a single hill on the 163km route, just outside of Macon, in a category four climb taken by polka dot climbers' jersey wearer Jonas Abrahamsen.
Friday's seventh stage is a 25km individual time-trial from Nuits-Saint-Georges to Gevrey Chambertin through open countryside and vineyards just to the south of Dijon.
Although those 25.3km are raced on largely flat terrain the nature of the excercise guarantees a shake up of the overall standings.
Evenepoel is the reigning time-trial world champion and could put pressure on Pogacar's lead.
