The Colombian clashed with the Team DSM duo of Cees Bol and Alberto Dainese as the sprinters tried to jostle for position on the way to the line in Scalea.
Gaviria flew out to the right of the track in an attempt to latch on to the DSM lead-out train in the final 300 metres, subsequently making contact with both riders, but all three miraculously avoided crashing out.
The incident made for another day of disappointment for Gaviria, who had mechanical issues in Stage 5 and publicly blamed his bike.
The results published following the stage had Gaviria all the way back in 105th, at the very back of the main bunch signalling the relegation.
"I didn't get to do the sprint I wanted today," Gaviria lamented after the finish.
"There was a bit of rough and tumble in the final but thankfully everyone stayed upright.
"The legs are really good so I'm hoping to get a big result soon in this Giro, we just need to be patient."
UAE director Fabio Baldato attempted to offer his take on the incident, but admitted it was difficult to know what really happened without speaking to his rider.
"It looks like from what I saw (Gaviria) was boxed in," Baldato told Eurosport.
"It's hard to really say what happened, we need to speak with him.
"The (DSM) guys were doing the lead-out for Dainese and he stopped in the middle of the road. Gaviria was trying to go around at the same time Dainese started.
"Sadly, that can happen in the sprint. Neither of the guys wanted to express what happened.
"They waited until last metre to come out because it was a really fast sprint with slight headwind. They all know that they need to come out at the last metre. And that's what happened. It's a sprint - it's a thing that can be."
The Giro d’Italia continues on SBS with Stage 7 from 7.30pm (AEST) on SBS On Demand, with the SBS broadcast starting at 10.50pm (AEST). WA viewers can tune in from 9pm (AWST) on SBS VICELAND.
