And he was far from the only Bridgestone rider in trouble; Gibernau was also sinking steadily down the order after leading so confidently - losing seventh to Rossi on lap 13 - while team-mate Loris Capirossi was demoted from sixth by his fellow Italian a lap later. Vermeulen then lost fifth to The Doctor on lap 16, forming an all-Michelin top five, as the Japanese rubber - which had been so strong in the wet - appeared to strike endurance problems.
But the four Honda young-guns up front - Pedrosa, Hayden, Melandri and Stoner - were showing no form of weakness, and their near 7-second lead over Rossi was insurmountable in the seven laps that remained. Instead, Rossi came under increasing pressure from Toni Elias, who had dropped to 12th in the early laps, but had then locked onto Rossi's rear wheel and been dragged up the order with the Italian.
Up front and Pedrosa was credited with leading laps 12 to 16 but - like Vermeulen, Gibernau and Melandri before him - was unable to break clear and his reign was eventually ended by Melandri, who dived inside at the final chicane on lap 17. That location, coming directly after the awesome fifth-gear right hander, was the most popular passing place on the track - and saw plenty more action in the remaining five laps.
Indeed, on the very next circulation, Stoner demoted Marco from the lead at that location - with the frantic victory battle now a three-way affair as an increasingly ragged Hayden slipped to the tail of the lead group and lost touch with the trio ahead of him.
Last October, Pedrosa and Stoner were again battling bar-to-bar for victory at Istanbul - although on that occasion it was in the 250cc class - but each looked every ounce a MotoGP winner as the 2006 race reached its climax. The pair of premier-class rookies sandwiching comparative veteran Melandri, a double race winner, as the last lap began.
But not for long: As the trio charged into the off-camber turn one for the final time, Pedrosa - who had lost a little ground through the final chicane - pushed his front Michelin a little too hard and his RCV suddenly folded under him, sending the 20-year-old spinning off-track. A distraught Dani jumped to his feet and was left to wonder what might have been as he resurrected 14th place at the chequered flag.
Meanwhile, Stoner - riding the 'standard' spec RCV - was still doing a brilliant job of containing factory supported Melandri, leaving no room for a pass and making no mistakes in his quest to become the joint youngest MotoGP race winner. But the grand prix was always going to be decided at the final chicane - and Melandri duly dived inside for the lead, with Stoner trying to brave-it-out around the outside of the Italian.
Melandri stayed wheel-perfect through the fiddly left-right-left complex that leads onto the start-finish straight - and Stoner frustratingly lost out on victory by just 0.2secs at the flag, but could still celebrate his first MotoGP podium in just his third race.
The win was exactly what Melandri needed after a poor, podium free, start to the season and the likeable Fortuna rider was justifiably ecstatic with his third MotoGP victory - which also moves him up to third in the championship.
Pedrosa's mistake left team-mate Nicky Hayden to inherit the final podium position and the Kentuckian has now taken the world championship lead, by just one-point from previous occupant Loris Capirossi, after the Ducati rider finished as the top Bridgestone rider in sixth.