However, Checa was soon pushed aside by Gibernau and Rossi, who would dominate the top two positions until lap 10 of 19 when Barros - having disposed of Checa as early as lap two - caught the pair and promptly slipstreamed past a surprised Rossi along the home straight, to sit directly behind race leader Sete.
Sadly for the Brazilian, who was on target for a podium at the very worst, his Dutch TT would end just one lap later when he was violently thrown from his Repsol Honda after an apparent mechanical failure locked up his rear wheel on the entry to a high speed right-hander.
The Brazilian's exit, by stretcher on his 200th GP, would promote Marco Melandri to third, but the young Italian would soon face a strong fight for the final podium position from Max Biaggi, Nicky Hayden, Colin Edwards and Ruben Xaus.
But over seven-seconds ahead there was an even tenser battle developing for victory between Gibernau and Rossi: Gibernau would lead right to the last lap, but Rossi was always close behind him and - after being thwarted by a clever change of racing line from the Catalan along the back straight - the Yamaha star finally made his move by diving inside at the hairpin.
Sete tried to stick it out around the outside and the two would ride side-by-side to the next turn, where they made contact - Gibernau's front wheel hitting the rear of Rossi's M1 and breaking the #15's front fender. That unsettled the Spaniard, allowed Rossi vital breathing room and the five-times world champion was able to hang on to the flag by 0.456secs.
Both Rossi and Gibernau seemed to realise the significance of the victory, with Vale perhaps even more spectacular in his celebrations than normal, while Gibernau looked totally crestfallen.
Although Sete would (just) maintain his usual compose in parc ferme and the podium it was clear to all, not least Rossi ('Sete is a little angry'), that it had been the most bitter of disappointments to lose so close to the finish.
Gibernau has also lost the riders' championship lead (he and Rossi and now level), while Honda have now been overtaken by Yamaha at the head of the manufacturers standings.
Indeed, while Rossi tried to surpress his joy, the most outwardly happy of the top three was Melandri (+10secs from Rossi), the former 250cc world champion taking his second premier-class podium in as many races.
The Italian had actually been closing on Gibernau and Rossi at one stage, but ran wide through the final chicane and would spend the rest of the race defending his position from Biaggi.