Mr. Vettel took the checkered flag at the Bahrain International Circuit (BIC), almost 7secs ahead of Lewis Hamilton taking his 2nd victory of the season and the lead in the F1 Drivers' Championship.
"Right from the first lap I felt the auto was there", Vettel said on the podium.
Vettel has now won two of three races and is seven points clear of Hamilton.
"We just have to make sure we keep it going".
Tyre provider Pirelli have altered the dynamic of the product delivered to all F1 teams this season and the early indication is Ferrari have adapted better than Mercedes. Then I lost position at the start. It was his 11th podium.
"I don't know the exact amount but it was more than one PSI", said Bottas of the extent to which the tyre pressures were wrong for the start. "I was oversteering all through the race". Fortunately for Mercedes he was able to hold off Ferrari's Kimi Räikkönen who finished fourth.
"Lewis seemed to have more pace, the gap between Seb and me was getting bigger, Lewis was putting pressure on me, so that made sense".
Hamilton was running second between team-mate Valtteri Bottas and Red Bull's Daniel Ricciardo on lap 13 when the safety auto was required for a collision between the Williams of Lance Stroll and the Toro Rosso of Carlos Sainz.
"The pitlane [situation] was really my fault, so apologies to the team for losing time there", said Hamilton.
The day proved to be hard for Red Bull Racing. And that's how the race finished.
The victory was the four-time world champion's second of the season and 44th of his career.
Hamilton's Mercedes teammate Valtteri Bottas will be behind the wheel on Wednesday. The 19-year-old Verstappen, who had driven so well from 16th place on the grid to finish third in China last weekend, climbed out and kicked the barriers in frustration.
On the next lap Lance Stroll in his Williams and the Toro Rosso of Carlos Sainz came together to bring out the safety vehicle and start a mad dash for the pits.
Bahrain Grand Prix victor Sebastian Vettel was also in action in his Ferrari, though on behalf of Pirelli rather than the Italian team. If anyone ever thinks I should feel happy with second then I don't really know what to say.
Hamilton's benchmark time was 2.5s slower than the lap recorded by Valtteri Bottas last Saturday to claim pole position.
There was some frantic action behind the leaders, with Fernando Alonso battling it out in midfield.
"I've never raced with less power in my life".
Vettel took victory at Bahrain by over six seconds from Hamilton, with Bottas third. He also sat out his time penalty at this point.
Mercedes boss Toto Wolff insists the team still believes in giving its drivers "equal opportunity" to race in 2017, though he admits it will have to consider team orders on a race-by-race basis now Ferrari is in the title fight.
Meanwhile, Alonso retired one lap from the end.