After 22 races with a win, Bottas finally returned to the top step of the podium as the Finn finished 14.5 seconds clear of Red Bull's Max Verstappen.
As for seven-time champion Hamilton, he finished fifth to fall six points behind the Dutch driver with six races of this epic F1 season remaining.
At one stage in the closing stages, though, it appeared as if Hamilton would claim third behind Verstappen, and so head to the next race in the United States just one point adrift.
Hamilton seemed set to run for the entire race on a set of intermediate tyres given the damp Istanbul Park track that persisted throughout the course of the entire 58 laps.
But Hamilton was called in after 50 laps to take on a new set of inters, giving up his third place at the time when he was 10 seconds clear of Red Bull's Sergio Perez in fourth and was seemingly comfortable on rubber that had worn to slicks.
Despite the fresh tyres, Hamilton soon suffered graining and was unable to make any impression on Perez and Ferrari's Charles Leclerc who came home fourth, leading to a series of frustrated messages from Hamilton to his team.
Heavy overnight rain combined with a light drizzle throughout the morning and the early afternoon, combined with cool temperatures, meant Pirelli's intermediate tyres were required from the off.
From pole position, inherited courtesy of Hamilton's 10-place penalty after the Briton had set the fastest time in qualifying, Bottas managed to keep Verstappen at bay on the short run down to the first corner.
Through turn one, AlphaTauri's Pierre Gasly banged wheels with Fernando Alonso in his Alpine, sending the veteran Spanish driver into a spin, earning the Frenchman a five-second time penalty.
That allowed Hamilton to make up one place after starting from 11th courtesy of his penalty before soon passing Aston Martin's Sebastian Vettel to settle into ninth after the opening lap.
Hamilton, however, then found his first roadblock in the form of AlphaTauri's Yuki Tsunoda before finally finding his way around the outside of the Japanese driver through the sweeping turn-three right-hander.
After quickly picking off Lance Stroll in his Aston Martin on the following lap to move up to seventh, Hamilton then found himself hunting down McLaren's Lando Norris, as was the case a fortnight ago in Russia.
But with the Mercedes possessing considerable grip, Hamilton made short work of his fellow Briton on lap 10 on the run down to turn 12.
With 20 per cent of the race run, Bottas had opened up a 2.6s lead over Verstappen, who was three seconds ahead of Leclerc, with sixth-placed Hamilton 16 seconds behind the Dutchman.
Two fastest laps followed from Hamilton before he found himself behind the second AlphaTauri of Gasly but the Frenchman was unable to hold the charging champion for as long as his team-mate Tsunoda, pulling off another move into turn 12 on lap 14.
At that stage, there was a 7.4s gap to Verstappen's fourth-placed team-mate Perez, who had vowed to give Hamilton a hard time should he find the 36-year-old in his mirrors.
Given the uneasy damp conditions, and with the inters starting to turn to 'slicks' and the leaders relatively on the same pace, by the halfway stage after 29 laps, Hamilton had closed to within 1.9s of Perez.
Three laps later and Hamilton finally had Perez in his sights half-a-second back before they went wheel to wheel through the final few corners of lap 34.
As they crossed the line to start lap 35, Hamilton had his nose in front, but Perez managed to regain fourth place into turn one.
After 36 laps, Verstappen was the first of the leaders to pit, with his Red Bull crew turning him around in 2.1s, followed a lap later by Bottas who had built up a handy cushion of almost five seconds prior to the stops.
Red Bull also brought in Perez on the same lap, finally releasing Hamilton into fourth behind new leader Leclerc, who had also yet to stop at that stage, followed by Bottas and Verstappen in second and third.
After 40 laps Hamilton was told to box. Asking 'Why?', he was told 'New inter is the way to go', to which he replied 'I don't think it is man', before requesting to 'stay out', to which he was told to do so for one more lap.
That remarkably turned another 10 laps, however. At a point when it appeared as if he could run to the end without stopping, Hamilton took on a new set of inters after 50 laps.
Three laps earlier, Leclerc's hopes of a race win had disappeared at the start of lap 47 as on fresh inters Bottas passed the Monégasque, prompting Ferrari to pit Leclerc.
Hamilton soon aired his frustration as Mercedes seemingly failed to take into consideration the graining that would occur on his tyres. "I told you man!" he said at one stage, and a stern "Leave me alone!" when informed of his gap to Leclerc.
Gasly eventually took sixth, followed by Norris, Ferrari's Carlos Sainz in eighth after starting 19th, with Stroll ninth and Esteban Ocon in his Alpine 10th, and without stopping to add to Hamilton's frustration.
What do you think?
Lewis should have listened and box when his team told him so.
10 laps later, Leclerc closed the gap with 1+ sec per round, and Max increased his advantage with 1+ second a round.
MB couldn't do anything else except overruling Lewis. Looking back (always easy), they (MB) should have overruled Lewis 10 laps earlier.
Wonder if Lewis admits his mistake when he looks back at the data now.
@Symanski: agree Lewis was too stubborn this race?
GPFans is a multi-platform, multi-language brand dedicated to Formula One coverage. We bring you all the ins and outs of the sport, 24/7, everything from up-to-the-minute news and features to the latest viral stories and clips.
We believe that a new generation of exciting, outspoken drivers will make F1 more popular than ever before, and we want to give our users access to as much of their heroes as possible, on and off the track. From Lewis Hamilton to Max Verstappen, Daniel Ricciardo to Sebastian Vettel, we provide in-depth analysis of every every Grand Prix in the season, from Australia to Abu Dhabi.
With Formula One under the new ownership of Liberty Media, how the sport is being covered is evolving, and GPFans will look to be at the heart of this progression into new media, as one of the fastest-growing sites covering the king of motorsports.