The Spaniard was amongst the strongest riders during the Mandalika weekend, qualifying second and leading the sprint until tyre wear dropped him to fourth.
After long-time leader Jorge Martin crashed out of Sunday's grand prix on lap 13, Vinales headed the field until the 20th tour when eventual winner Francesco Bagnaia came through.
Vinales trailed Bagnaia home in second by 0.306 seconds to score his third Sunday rostrum of the season and feels a first win since the 2021 Qatar GP when he was a Yamaha rider is close.
“Well, we have done the maximum with what we have,” Vinales told motogp.com’s After the Flag last Sunday.
“That’s our objective. We know still we need to work a little bit.
“We start to get on the correct speed, but we know we have some issues with the tyre life, especially here – not only in other tracks.
“So, I think it’s a matter of time. We need to keep working, putting up good weekends in a row and it will come. I’m completely sure.”
Vinales was quickly dropped by Martin in the early stages of last Sunday’s grand prix but says matching the pace of the Pramac Ducati would have shredded his Aprilia’s tyres.
“Maybe I could have followed Jorge for five, six laps,” he added. “But if I tried it, my rear tyre was gone. So, I needed to slow down.
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“This was not my pace. I knew the race was very long, we knew our objective. So, I just keep concentrating on trying to not hurt the rear tyre and make it to the end.”
Vinales got another solid launch off the line in Indonesia as Aprilia has managed to improve this area of its RS-GP over the last few rounds.
However, it still proved no match for Martin’s Ducati as he leapt up from sixth to first at Turn 1, and Vinales says there is no chance for Aprilia to counter this in the remainder of the season.
“He just passed in another speed,” Vinales said of Martin’s start. “It’s amazing how they start, but we know why. They are much lower on the centre of gravity, so they can use much more power.
“But we cannot bring it now because we need to modify the chassis, so it’s going to arrive next year.”