Vettel held off the charge of Mercedes' Valtteri Bottas to take victory in his 200th grand prix, but the occasion was soured after a member of Raikkonen's pit crew was taken to a medical center after an incident during lap 36 of the race.
Raikkonen attempted to leave a pit stop before all four of his tires were safely attached and his rear left wheel hit a member of the crew, with video showing the mechanic's leg buckling horribly.
The Finn retired from the race while medical assistance was issued to the mechanic.
"Bittersweet WIN for #Seb5 and for the Scuderia, great performance but we are all waiting for the medical bulletin for our mechanic #BahrainGP," Ferrari tweeted at the end of the race.
Ferrari later tweeted that the mechanic, Francesco, had suffered a shinbone and fibula fracture.
Ferrari has been hit with a €50,000 ($61,410) fine by governing body FIA for exiting the pit stop "in a manner endangering team personnel and causing injury."
This follows the €5,000 ($6,100) penalty the team received Friday after Raikkonen left a pit stop during practice without one of his wheels being properly attached.
"I don't know what shape he's in," Raikkonen said after Sunday's race. "For sure, not great for him."
A traffic light system is used to tell the driver when it's safe to leave the pit stall.
"I go when the light is green, I don't see what happens behind," added Raikkonen. "My job is to go when the light changes."
Ferrari decided after the race that a mechanic should join Vettel on top of the podium.
"We chose to take one of our mechanics up onto the podium as a mark of respect to our colleague Francesco who was injured during the pit stop," said team boss Maurizio Arrivabene.
"The whole team hopes he recovers quickly."
Reigning world champion Lewis Hamilton finished third in a pulsating race, which saw Vettel squeeze the maximum out of tires he was forced to use from lap 18 of the 57-lap race to beat Bottas by just 0.699 seconds.
With 10 laps to go Vettel told the team radio he had "everything under control," but quipped during a podium interview: "That was a lie!"
"Fortunately he ran out of laps," continued four-time world champion Vettel, referring to Bottas' challenge, before adding: "I'm really happy."
"We had nothing to lose trying to stay out and trying to win," explained Vettel as he analyzed his long run on deteriorating tires.
"It worked, just! If you manage to get the win in these conditions, it makes it better."
Hamilton started ninth on the grid and battled his way into contention before ultimately finishing adrift of the leading two drivers.
In one thrilling maneuver during the race Hamilton overtook three drivers in one go.
The Briton was hampered by radio issues throughout the race and sounded frustrated during communications with his crew.
But Hamilton insists it was a satisfactory result.
"I'm happy," he said. "I started ninth so third isn't bad at all."
Vettel's win pushed him up to 50 points in the drivers' standings, 17 ahead of Hamilton, with Bottas third on 22 points.