Rosberg dived down the inside of Raikkonen at Turn 2 to snatch third on the 38th lap of the race - but as he did so slid into the side of the Finn's Ferrari.
Rosberg was handed a 10-second time penalty for the clash, but with Raikkonen's car hampered, the German was able to pull enough of a gap to still secure the final step of the Sepang podium, with the pair split by just over three seconds at the flag.
"It was impossible to give him more power," Ferrari team boss Maurizio Arrivabene explained when asked if there was any way Raikkonen could have prevented Rosberg from clinching third.
"Due to the impact with Nico, Kimi lost part of the floor and part of the front wing. From the calculations we have with the engineers, he lost more or less 10 points [of downforce] - so it was quite impossible for him to catch up in this situation.
"Even in such a difficult situation he was doing very good lap times - even with a rather severely damaged car. We tried from the pit wall to do our best, and also with regards to the strategy. We were aggressive - but so were others.
"Yes, it is a pity that Kimi didn't finish on the podium. But with the impact all chances were gone."
With Sebastian Vettel retiring on the opening lap, Ferrari were restricted to just 12 points in Malaysia – equalling their second-worst return of the season. They now trail Red Bull by 46 points in the fight for second in the constructors' championship – while Raikkonen jumped ahead of Vettel and into fourth in the drivers' standings.
"It will be tough – but we will fight," Arrivabene added when asked if Ferrari can still secure second. "This is our job and this is what we have to do."