The German seemed to be positioned too far back going into the final 500m, but found himself with a clear run to the line to win the stage and extend his lead over Groenwegen in the overall classification to eight seconds.
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While Kittel’s stage win on the opening day of the race had been set up by a superb lead-out effort, this one was not so simple.
The Quick-Step Floors train was well-positioned going into the final 5km, before being swamped with 2km to go, and further caught out by a tight bend just before the final kilometre.
That left Kittel positioned further back than he might of liked going into the final sprint, with Groenewegen being in a perfect position at the front of the pack with 250m to go.
However the Dutchman didn’t seem to have the legs, fading in the final 50m and holding up the charge of Mark Cavendish (Dimension Data) in the process.
Kittel, meanwhile, had a clear run on the other side of the road, accelerating off the wheel of lead-out man Matteo Trentin to come around Groenewegen and John Degenkolb (Trek-Segafredo) in the final few metres of the stage.
Watch: highlights of stage two of the Dubai Tour
The day’s break consisted of five riders: Mark Christian (Aqua Blue Sport), Simone Andreetta (Bardiani-CSF), Jempy Drucker (BMC Racing), Peter Williams (One Pro Cycling), and Yousif Mirza (UAE Abu Dhabi).
The escape went after 20km, quickly building up a gap of more than four minutes on the flat 188km stage between the Dubai International Marine Club (DIMC) and Ras Al Khaimah.
Drucker won both of the intermediate sprints, picking up three bonus seconds at each, before dropping back to the peloton to leave a four-rider group in front.
The break’s advantage steadily fell as Dimension Data and Quick-Step Floors sat on the front of the peloton, dropping under a minute for the first time with 30km to go.
From that point the gap to the peloton remained steady at around the 50 second mark for a number of kilometres, with the break only being caught with 11km to go as the sprinters’ teams started to battle for position.
With 5km remaining the sprint trains really began to emerge as LottoNL-Jumbo, working from Groenewegen, battling on their own on the left of the road as Dimension Data and Quick-Step stayed on the right.
That was a mistake from the Dutch team, with Quick-Step accelerating on the front of their side of the peloton, forcing LottoNL-Jumbo back down the pack.
However with 2km remaining it was then Quick-Step who got swamped, as Trek-Segafredo hit the front hard with Kittel falling back down the pack.
But the front of the peloton was constantly changing through the final kilometres, with only a tight left hand turn with 1.5km to go stringing the bunch out, with all of the big-name sprinters in close attendance.
Dimension Data led under the flamme rouge, before Groenewegen hit the front at what seemed like the perfect timing with 200m to go.
However the Dutchman faded in the final 50m, and while that held up riders behind him, including Cavendish, Kittel had a clear run to the line on the left of the road to take his second successive stage win.
The Dubai Tour will continue with stage three tomorrow, 200km from DIMC to Al Aqah, with another sprint finish expected.
Dubai Tour 2017, stage two: DIMC to Ras Al Khaimah, 188km
1. Marcel Kittel (GER) Quick-Step Floors, in 4-25-33
2. Dylan Groenewegen (NED) Team LottoNL-Jumbo
3. Jakub Mareczko (ITA) Wilier Triestina
4. John Degenkolb (GER) Trek-Segafredo
5. Sacha Modolo (ITA) UAE Abu Dhabi
6. Juan José Lobato (ESP) Team LottoNL-Jumbo
7. Mark Cavendish (GBR) Dimension Data
8. Riccardo Minali (ITA) Astana
9. Marco Maronese (ITA) Bardiani-CSF
10. Adam Blythe (GBR) Aqua Blue Sport, all same time
General classification after stage two
1. Marcel Kittel (GER) Quick-Step Floors, in 8-31-26
2. Dylan Groenewegen (NED) Team LottoNL-Jumbo, at 8 secs
3. Nicola Boem (ITA) Bardiani-CSF, at 13 secs
4. Jean-Pierre Drucker (LUX) BMC Racing, at 14 secs
5. Thomas Stewart (GBR) One Pro Cycling, same time
6. Mark Cavendish (GBR) Dimension Data, at 16 secs
7. Jakub Mareczko (ITA) Wilier Triestina
8. Yousif Mirza (UAE) UAE Abu Dhabi
9. Silvan Dillier (SUI) BMC Racing
10. Peter Williams (GBR) One Pro Cycling, all same time