With Nakagami sliding across the middle of the track on the approach to turn eight, Vinales was left with nowhere to go due to his positioning which was on the outside of the Japanese rider.
Still, Vinales’ lap times after that were very impressive, however, the Spaniard was also frustrated by technical issues that arose in FP3, while a misunderstanding with the team at the end of FP1 saw him return to pit lane thinking he would fit new tyres, which was instead not the case.
Vinales said: "Yeah it was good [race pace]. When I went to the box and saw the lap times, I could have been on the podium again.
"Not fighting with Bastia [Bastianini] and Pecco [Bagnaia] but between Bastia and Aleix [Espargaro]. I think like in Misano I was able to follow them until mid-race and then drop again.
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"Well, I’m a little bit disappointed because this weekend it was very important. Last year [in Aragon] I was very slow and this year I felt very fast since FP2 and then a lot of technical problems, misunderstandings and it’s something I don’t like because I gave my best.
"This weekend I didn’t feel like we worked well. We need to analyse and we need to think and improve for Japan because I think our opportunity will come to win the race so we need to be ready. I think this weekend was a good opportunity because the bike was working well."
Vinales keen to assist Espargaro by taking first MotoGP win with Aprilia
Also involved in a clash with Marquez during the opening lap in Aragon was series leader Fabio Quartararo.
The Yamaha rider crashed after hitting the back of Marquez and has subsequently seen his championship lead slashed from 30 points to just 10.
Espargaro, who had seen his title challenge begin to fade in recent races, has also closed to within a win and is now only 17 points back thanks to his third place in Aragon.
With every race weekend from now until the end of the season likely to prove crucial in the title fight, Vinales is keen to help his fellow Spaniard by being at the front and taking wins.
"I will not say comeback because when I see the lap times I am there," added Vinales when asked if he needs to make a ‘comeback’ from Aragon. "Basically do a good Friday, a good Saturday and start in the front.
"Then, we always have the chance to be on the podium. For me, seeing that I was there on the lap times, equal to Aleix, it makes me feel very strong as this is his best track.
"I think it’s very important for us and for Aprilia - now I’m talking as a team - I’m sorry for Fabio [Quartararo] because the crash was very nasty and I hope he is okay but we are back on the fighting.
"Now I need to be in the front. I need to be in the front fighting and help Aleix as much as I can. The way to help him is to try and win races."