While Vettel swept to victory in Sunday's Bahrain Grand Prix, Raikkonen was once again unable to match his team-mate for pace, finishing 22 seconds adrift in fourth place after passing Williams' Felipe Massa twice.
Mercedes rival Lewis Hamilton staged a late charge to finish second after picking up a time penalty.
The three-time world champion said the penalty was a setback, but that his Mercedes may not have been fast enough to overhaul the triumphant Ferrari of Sebastian Vettel.
Hamilton was running second between team-mate Valtteri Bottas and Red Bull's Daniel Ricciardo on lap 13 when the safety vehicle was required for a collision between the Williams of Lance Stroll and the Toro Rosso of Carlos Sainz.
A slow stop for Bottas delayed Hamilton slightly anyway and he dropped behind the Red Bull, and was then hit with a five-second penalty for delaying Ricciardo.
"It's been a really great day for me". "Which I think is what racing should be about".
The undercut worked to perfection with Vettel taking charge of the race - even though the safety auto was deployed moments later after hapless Canadian rookie Lance Stroll crashed into the Toro Rosso of Carlos Sainz - with 12 of the 57 laps gone. Kimi Raikkonen took fourth for Ferrari after a poor start ahead of Daniel Ricciardo, who was in the mix at the start but lost ground when he switched to soft tyres for the second stint.
"The pit lane (incident) was really my fault so apologies to the team for losing the time there ... but I gave it everything I could".
"From then on we were on the back foot", he said.
Vettel completed the 57 laps of the 5.4-kilometer (3.4-mile) track in 1 hour, 33 minutes, 53 seconds, for his third win in Bahrain after success with Red Bull in 2012 and 2013. The incidents were coming fast, with 18-year-old Lance Stroll hit from the side on lap 13 by Carlos Sainz Jr. - forcing the safety vehicle to come out.
Vettel, who was held up behind Bottas early on was the first of the major players to pit and when Ricciardo's team-mate Max Verstappen suffered rear brake failure on the 12th lap and crashed.
Both Mercedes drivers used the safety vehicle incident to pit for new tires, but Hamilton held up Ricciardo. On lap 36 Vettel caught Raikkonen and the Ferraris traded position, giving Vettel a clear road to hunt down Hamilton who was still in the lead.
Valtteri Bottas says he understands why Mercedes ordered him to let teammate Lewis Hamilton pass at the Bahrain Grand Prix, but admits he did not like doing it. There was more misery for McLaren after Stoffel Vandoorne failed to start while Fernando Alonso failed to finish.