Starting from seventh on the grid, the Anglo-American made a strong start and was up to fourth by the first corner. He then passed Nicky Hayden to move in to third place on lap four, behind Casey Stoner and Dani Pedrosa.
Hopkins tried to chase down the two in front of him, but the gap was already too large and he had to settle for a race against the clock as he was never troubled by another rider for the remaining laps.
An emotional Hopkins eventually crossed the line with his front wheel high in the air to celebrate his best-ever result at Valencia, his fourth podium of the season and fourth overall in the 2007 riders' world championship.
"I have just got to thank everyone at Suzuki - that is my first and foremost task," said Hopper, who will race for Kawasaki next season. "To every member at Suzuki I want to pass on my ultimate thanks to them, Suzuki has given me my life in MotoGP and established my career and I just cannot show enough gratitude to them.
"Today the tyres and the bike worked awesome and I just went for it from the beginning!" he recalled. "I got a good start and then got around Nicky Hayden, but from there it was a pretty lonely race. I just had to push myself against the clock and make sure I pulled away from the riders behind me. I succeeded in that but it was very emotional on the last few laps with that comfort and I had to concentrate real hard to keep focused!
"It's a great result because my Mum, sister, fiancée and her family are all here today so it was an unbelievable feeling when I crossed the line - it was a great way to end the year. I would have liked to have put the bike on the top step for Rizla Suzuki and especially all my crew, but that's for Dani and the home fans today!
"I just want to say thanks once again, it's been a fantastic five years and I've had a top time, now I just want to take it all in tonight and have a good time with the boys!" he concluded.
Hopkins finished his most successful season in MotoGP two points ahead of Marco Melandri and ten points clear of team-mate Chris Vermeulen, who fought his way up from 12th on lap one to sixth at the finish.
"I felt like I had the speed to run with John, but he had a much better advantage after the first few laps," said Chris. "We finished sixth in the end and sixth in the championship, it's been a good season and we have improved a lot this year. We have a number of new things coming so it looks like being a very exciting future.