The Belgian rider took advantage of the lack of big-name sprinters once more to cross the line ahead of Trek-Segafredo‘s Fabio Felline and FDJ’s Kevin Reza.
A big crash within the three kilometre mark saw Steven Kruijswijk drop out of the race with what looks like a broken collarbone, with several other riders down on the road too.
The day was a slow one, travelling 171km between Viveiro and Lugo with only one categorised climb along the way, during which the peloton mostly rode in wet conditions.
Machado wasn’t going to be left to claim the win, though, with the peloton calmly reeling him in within the final 20km of the stage, with the peloton brought to life by an attack from Mont Ventoux stage winner Thomas de Gendt (Lotto-Soudal)
As the teams set themselves up for a sprint, with Adam Hansen doing much of the pace setting for Lotto-Soudal, Simon Clarke (Cannondale-Drapac) and Philippe Gilbert (BMC) tried their hand off the front.
With none of the peloton’s major sprinters in the pack, the duo looked as if they could hold off the weakened trains of the leading teams, but with under a kilometre to go they were brought back in and the fast men played it out.
Meersman took to the front early in the last 200m, followed by Felline who couldn’t quite move around him to get to the line first.
Alejandro Valverde (Movistar) came to the front of the peloton in the final three kilometres and stayed there to finish sixth and provisionally to stay in second place ahead of Chris Froome.
Vuelta a España stage five, Viveiro – Lugo (171km)
1. Gianni Meersman (Bel) Etixx-Quick Step, 4-16-41
2. Fabio Felline (Ita) Trek-Segafredo
3. Kevin Reza (Fra) FDJ
4. Luis Leon Sanchez (Esp) Astana
5. Zico Waytens (Bel) Giant-Alpecin
6. Alejandro Valverde (Esp) Movistar
7. Romain Hardy (Fra) Cofidis
8. Jean-Pierre Drucker (Lux) BMC
9. Kenneth Vanbilsen (Bel) Cofidis
10. Jose Gonçalves (Por) Caja Rural, all same time
Overall standings after stage five
1. Darwin Atapuma (Col) BMC, 17-39-52
2. Alejandro Valverde (Esp) Movistar, at 28s
3. Chris Froome (GBr) Team Sky, at 32s
4. Nairo Quintana (Col) Movistar, at 38s
5. Esteban Chaves (Col) Orica-BikeExchange, st
6. Samuel Sanchez (Esp) BMC, at 1-07
7. Ruben Fernandez (Esp) Movistar, at 1-10
8. Leopold Konig (Cze) Team Sky, at 1-12
9. Peter Kennaugh (GBr) Team Sky, at 1-14
10. Gianluca Brambilla (Ita) Etixx-Quick Step, at 1-22