Evenepoel was in the midst of a tame 189-kilometre journey to Tomares before a late puncture preceded an attack from GC rival and defending champion, Primož Roglič.
Roglič appeared primed to lead a quintet to the line and overturn his overall deficit to Evenepoel, only to crash inside the final 100 metres and cede the stage to Mads Pedersen (Trek-Segafredo).
The Slovenian was still able to cross the line ahead of Evenepoel, but only be eight seconds after the latter's puncture took place inside the three-kilometre 'safety zone'.
Evenepoel was initially timed five minutes adrift of Roglič but, alongside Alejandro Valverde (Movistar), was the beneficiary of a rule which awards the rider a time in line with the bunch.
It was a slice of "good luck", according to the Belgian, who denied faking the incident in a bid to limit his losses in the race for the red jersey.
"Nobody can say anything," Evenepoel said after the race. "I'm not a guy who is going to fake such things.
"We were fighting for position, I was sitting not at the front, but also not at the back, just in the middle of the group.
"I felt really good, I also wanted to fight for the stage win, but I had a flat tyre at the back. I felt immediately that the grip was going. I had to change it."
"I wasn't sure if there was the three kilometre rule," he added. "But in the end, Klaas [Lodewyck, sports director] told me over the radio that there was, so that reassured me and calmed me a little bit."
The 22-year-old now leads Roglič by 1'26" ahead of Stage 17, though it remains to be seen whether the three-time champion will line up in Aracena.
Roglič sustained injuries to his right elbow, hip, knee and ribs in the crash with Fred Wright (Bahrain Victorious), but a decision won't be made until one last consultation with the medical doctor.
"All investigations for today have been carried out," Jumbo-Visma said on Twitter.
"Tomorrow morning, the team will decide in consultation with the medical doctor whether Primož will continue his fight this @lavuelta."
La Vuelta continues tonight with Stage 17 which concludes with a summit finish to Monasterio de Tentuda. Watch from 10:50pm (AEST) on SBS and SBS on Demand for all the action.
