Vettel now leads Hamilton by 17 points after two of the 21 races. Hamilton finally stopped a lap later, swapping his soft tyres for mediums. With the VSC on track, Verstappen managed to crawl back into the pits. A Virtual Safety Car was called so the Red Bull could be recovered, cooling things down after a heated start.
Verstappen lunged underneath Hamilton on the 220mph turn 1 charge before inadvertently colliding with the Mercedes auto. It was more consistent on one lap but also in the race. Vettel pitted from the lead on lap 18 with the aim of running a two-stop strategy, but Ferrari had to change its plans when it became clear Mercedes would last the race on a one-stop. The Ferrari continually lost ground into the final five laps as the gap between the silver bullet behind him shrunk to under two seconds.
A frustrated Vettel finally burst past the defensive Hamilton, on his original tyres, to re-gain the lead on lap 26.
"With Bottas' pace I thought he would catch me. I feel sorry for him and hope he's going to be OK soon".
Kimi Raikkonen, who was in the third position had to end his race after an incident in the Ferrari pitstop.
This left Bottas as the lone driver to challenge a rapidly fading Vettel.
The system turned on a green light to signal that all four wheels had re-fitted tyres, but the left-rear tyre was stuck and had not been removed.
The injured mechanic has been taken to hospital for treatment.
"It's disappointing, but I think what is positive is that actually the race pace we had was more competent and we could put a bit more pressure on them than we expected to". Hamilton, who voiced his frustrations over the radio on several occasions, completed the podium in third place, 8.5 seconds behind the front pair.
"The race is 57 laps and Sebastian got to the flag the quickest so they won", said Bottas.
"Daniel commented that even in the two laps that he was able to do, he was able to close pretty comfortably on (Ferrari's) Kimi (Raikkonen)". The Finn tried tailing through the middle sectors, but was unable to get another chance to pass.
It seems as though he's in good spirits after posting a picture to Instagram saying: "Surgery ok".
Fernando Alonso and Stoffel Vandoorne gave McLaren, now with Renault engines, a second successive double points finish in seventh and eighth respectively to lift the team to third overall.
"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.
The former champions are now the only team yet to score points this season after Force India's Esteban Ocon secured 10th place. Hamilton crossed the line another 5.8s behind. Sergio Perez and Brendon Hartley spent much of the race scrapping, having also made contact at the first corner.
Magnussen dropped to 10th when he came in for his second stop and wasn't impressed with his team-mate Romain Grosjean.