The Honda Gresini rider had been absent from the podium since before the summer break, at Laguna Seca, but qualified third on the grid prior to fighting his way past Kawasaki's
Randy de Puniet and factory Honda rider
Dani Pedrosa by the midway point of the 21 laps.
Melandri then looked to have a chance of challenging for victory as he trimmed future team-mate
Casey Stoner's advantage down to less than a second, but the Ducati star responded to the threat and Marco was forced to settle for a well earned second.
"This podium feels like a victory to us," beamed Melandri. "I had never been on the podium here at Sepang and I don't think it is a circuit that suits my riding style or our bike. Anyway, today proved that when you have a great package of bike and tyres, as I did today, you can be fast anywhere.
"I was nervous before the start because I tried to move a little bit the valve for the drink but I made a mistake and pulled it out!" explained the Italian. "The water was continually coming out so I tried to disconnect the tube but for the first two laps every time I was braking the water that still was in the tube was coming out inside the visor so it was difficult and I was a bit nervous. But after that I took my rhythm and I was pretty fast.
"I caught Dani, I tried to catch Casey but I had a big moment with the front end and I lost almost one second in one lap," he revealed. "After I tried to catch him back and I pushed a lot. Then, at two laps to go, when it was not possible to catch him, I thought it was really very good for me to be second so I just want to say thanks to Fausto and my team for these three years we have raced together."