Merlier, 28, riding for Alpecin, finished ahead of two Italians, European champion Giacomo Nizzolo and Elia Viviani, to claim his fourth win of the season.
Groenewegen has not raced since August 5 when he provoked a crash in the sprint at the end of the first stage in Poland that left fellow Dutch sprinter Jakobsen with injuries that included several skull fractures.
However, Jakobsen's team said Tuesday his condition had improved further and that he would be moved to a hospital in his homeland.
Tour de France 2019: Australian Caleb Ewan picks up first-ever stage win as Julian Alaphilippe retains yellow jersey
Ewan timed his explosive burst to perfection, catching and overtaking Dutch sprinter Dylan Groenewegen right on the line after a long home straight. Elia Viviani was third on a finish designed for the pure sprinters
Dylan Groenewegen beat Australia's Caleb Ewan in a photo-finish to make up for the pain of falling on stage one on the Brussels home straight.
Tour de France 2019: Surprise winner Mike Teunissen finishes first in opening stage as final kilometre collision takes out chasing pack
Teunissen edged Peter Sagan by a few centimetres on a slightly uphill sprint in a photo finish at the winning line, the Slovak will wear the green sprint points jersey Sunday after he won the early intermediate sprint leaving him and Teunnissen on 50pts each
Chris Froome claims a hat-trick of Tour de France titles winning the 'closest and most challenging' race
Here's a look into Stage 21 that saw Chris Froome winning the Tour de France 2017 and Netherlands' Dylan Gronewegen winning his maiden stage.
Tour de France 2017: Chris Froome wins his fourth title, Dylan Groenewegen claims maiden win in Stage 21
Chris Froome secured his fourth Tour de France title at the end of the 21st and final stage won by Dylan Groenewegen on Sunday and said it was a huge honour to be amongst cycling's greats.
Marcel Kittel, the 29-year-old German, was at his imperious best in winning a fifth sprint finish out of six, once again making it look easy.
Marcel Kittel, the burly German, cantered to a fourth stage win of the Tour at the end of Tuesday's 178 kilometres 10th stage from Perigueux to Bergerac, as Chris Froome retained his overall lead.