The Frenchman made a storming start for Lotus from fourth on the grid to seize the lead and stay in front for half the race before Red Bull's strategy put 2012 world champion and series leader Sebastian Vettel in the driving seat.
Even then a second place might have been Grosjean's consolation, had he not been held up by backmarkers and then overtaken on the penultimate lap by Red Bull's Australian Mark Webber on fresher tyres.
"I thought it was the day that the first victory was coming," Grosjean, a former GP2 champion who has a chequered past, told reporters after appearing on the Suzuka podium.
"I said 'our car is beautiful today, it's going to be good..."
The Frenchman's 2012 season was littered with first corner crashes, including one that brought him a race ban for the Italian Grand Prix, but Sunday's start showed how much progress he has made.
"When I dropped the clutch I said 'Whoah, that's a good one, come on, come on go for it'. Amazing," he said.
"Then when you're leading it makes the thing easier on the first stint. We were very quick on the option (tyre).
"I think it would have been nice with Mark until the end of the race but we caught some slower cars, lapped cars, and they really blocked me a lot. I lost the position against Mark. I don't know if I could have held him until the end."
The race was a marked contrast to last year's at Suzuka, when a furious Webber branded Grosjean a "first-lap nutcase" and berated him after they collided in the opening seconds.
Webber had been on the front row last year as well, alongside Vettel, but his hopes were wrecked by the Frenchman.
The crash left him fighting back to ninth.
The Australian, who is leaving Formula One at the end of the season for a new career in sportscars with Porsche, was far more complimentary on Sunday about his old sparring partner.
"I think it's very clear that Romain has a very different mental approach to the job at the moment this year," he said.
"He's driven some quite strong races, putting together the whole weekend which is a sign of a driver starting to get a bit more relaxed and confident. A lot fewer mistakes, not just in races but in practice.
"You know, we're not here to blow smoke up his arse but in the end he's doing a very good job this year and it's a big step for him...I hope he doesn't improve too much more before the end of the year."
Sunday's third place was Grosjean's fourth podium finish of the season and his second in a row after being overshadowed for most of the year by team mate and 2007 world champion Kimi Raikkonen.
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