The German sprinter took victory at the end of a hectic stage three that saw crosswinds and a sandstorm hit the peloton, and race leader Marcel Kittel (Quick-Step Floors) left with a bloody face after allegedly being elbowed by an Astana rider.
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However it was more poor positioning that cost Kittel at the end of the stage, as he was unable to challenge Degenkolb, who came off the wheel of Dimension Data‘s Reinhardt Janse Van Rensburg to win the stage, with Sonny Colbrelli (Bahrain-Merida) in third.
As had been the case on previous days, it was a small breakaway group that went clear on day three of the Dubai Tour, consisting of, Mark Christian (Aqua Blue Sport), Luka Pibernik (Bahrain-Merida) Loïc Vliegen (BMC Racing), and Alex Dowsett (Movistar)
That group quickly built up a lead of nearly six minutes, but that advantage was swiftly reduced as crosswinds and a sandstorm hit the race with around 130km of the 200km stage remaining.
That was a cue for the pace to go up in the peloton, with echelons forming and splits in the group that saw race leader Marcel Kittel caught out.
However the gaps between the various groups were never more than a handful of seconds, and despite a hard effort by Dimension Data to pull the front group (containing Mark Cavendish) clear, the peloton eventually came back together.
That set the race up for a straight pursuit between the peloton and the four-man break, with the break taking an advantage of around two minutes into the final 35km.
Watch: essential guide to the Dubai Tour, Tour of Oman, and Abu Dhabi Tour
That advantage held steady for around 10km, before the sprinters’ teams really started to accelerate, bringing the gap under a minute for the first time with 19km to go.
The four-man break still had enough of an advantage to contest the final intermediate sprint, which was won by Dowsett, and made the peloton work hard to make the catch.
With the break caught, there was a brief counter-attack by BMC Racing‘s Daniel Oss, but that did nothing but increase the speed of the lead-out trains as Dimension Data raised the pace just before the flamme rouge.
Into the final 200m, and with Cavendish positioned too far back, it was up to Janse Van Rensburg to fly the Dimension Data flag, and although the South African put in a strong effort through the final few hundred metres, it was Degenkolb who took a narrow victory.
That result moved Degenkolb up to third place in the overall standings, two seconds behind Dylan Groenewegen (LottoNL-Jumbo) and ten seconds behind Kittel, and in a strong position to take overall victory with an uphill finish on stage four that should suit play to his strengths.
Dubai Tour 2017, stage three: DIMC to Al Aqah, 200km
1. John Degenkolb (GER) Trek-Segafredo, in 4-03-08
2. Reinardt Janse Van Rensburg (RSA) Dimension Data
3. Sonny Colbrelli (ITA) Bahrain-Merida
4. Juan José Lobato (ESP) Team LottoNL-Jumbo
5. Riccardo Minali (ITA) Astana
6. Jean-Pierre Drucker (LUX) BMC Racing
7. Elia Viviani (ITA) Team Sky
8. Dylan Groenewegen (NED) Team LottoNL-Jumbo
9. Adam Blythe (GBR) Aqua Blue Sport
10. Daniele Bennati (ITA) Movistar
General classification after stage three
1. Marcel Kittel (GER) Quick-Step Floors, in 12-34-54
2. Dylan Groenewegen (NED) Team LottoNL-Jumbo, at 8 secs
3. John Degenkolb (GER) Trek-Segafredo, at 10 secs
4. Nicola Boem (ITA) Bardiani-CSF, at 13 secs
5. Jean-Pierre Drucker (LUX) BMC Racing, at 14 secs
6. Reinardt Janse Van Rensburg (RSA) Dimension Data
7. Alex Dowsett (GBR) Movistar
8. Thomas Stewart (GBR) One Pro Cycling, all same time
9. Jakub Mareczko (ITA) Wilier Triestina, at 16 secs
10. Mark Cavendish (GBR) Dimension Data, at same time