He was not without pressure though, as the Lotus of Kimi Räikkönen climbed the field, having started in eleventh place, and challenged for the lead before finishing second.
Hamilton started on the front row, but pitstop errors and degrading tyres left him eighth; his McLaren teammate, Jenson Button, retired with two laps remaining.
[9] The decision to hold the race despite ongoing protests and violence[10] has been described as "controversial" by Al Jazeera English,[11] CNN,[12] AFP[13] and Sky News.
[4] As the 2011 race was cancelled, the teams arrived in Bahrain with no data on how the Pirelli tyres introduced for the 2011 season would behave at the Sakhir circuit.
[20] Similarly, the Drag Reduction System (DRS) was introduced for the 2011 season, and consequently had never been used at the Bahrain International Circuit in a race.
Maldonado became the fourth driver of the 2012 season to receive a gearbox penalty, after Sergio Pérez, Kimi Räikkönen and Lewis Hamilton all made similar changes in Australia, Malaysia and China.
Vettel was second-fastest, three-tenths behind the McLaren driver, while Paul di Resta in the second Force India was third, having switched to the softer "option" tyres in the last ten minutes.
Several other drivers, including Jean-Éric Vergne, Vitaly Petrov, Pastor Maldonado, Timo Glock and Daniel Ricciardo also emerged, setting lap times within the first five minutes of the session starting.
After the initial rush of the first fifteen minutes, Jenson Button emerged as the fastest man on the circuit before being surpassed by Mark Webber moments later.
Jean-Éric Vergne was the first driver to leave the pits, leading a group of fourteen, but they returned to the lane immediately; with the cars being switched to race specification the night before, further installation laps were needed.
He was followed closely by teammate Nico Hülkenberg, with both drivers following an extensive testing program, having missed the second free practice session; after one hour, they had completed forty-three laps between them.
Toro Rosso driver Jean-Éric Vergne spent most of the period facing the threat of elimination, even though he was as high up the order as sixth at one point, after putting on the softer tyres.
[36] The HRTs of Pedro de la Rosa and Narain Karthikeyan finished in twenty-second and twenty-fourth; both were inside the 107% margin (1:40.380), but they were still four seconds off the pace of Sergio Pérez, the fastest man in Q1.
The seventeen remaining drivers went straight out onto the softer tyres for Q2, with Lewis Hamilton and Nico Rosberg quickly establishing themselves at the top of the timing charts.
Meanwhile, Bruno Senna's final lap was marked by sector times that suggested he would also advance to Q3, but a mistake at Turn 13 cost him dearly, and he had to settle for fifteenth overall.
Unable to challenge the other teams in terms of raw pace, Kovalainen finished the period in sixteenth after Pastor Maldonado was stricken by a KERS issue, and failed to set a lap time.
[37] With the ban on refuelling in place since 2010, drivers are now able to complete Q3 in a low-fuel configuration, making Vettel's time a more-appropriate benchmark for comparison purposes.
Initial speculation at the start of the period suggested that Sergio Pérez would not set a lap time, but the Mexican driver took to the circuit and finished eighth overall.
[42] Shortly after qualifying ended, speculation in the media suggested that Force India had received no coverage during the broadcast as punishment for withdrawing from the second free practice session.
[44] Bernie Ecclestone explained the team's lack of coverage as the television director wanting to concentrate on the pole sitter "rather than somebody who was going to be tenth".
Jenson Button slipped to 6th by turn one, Bruno Senna was up to 10th from 15th while his teammate Pastor Maldonado was 15th after lap 1 following his gearbox penalty which forced him to start from 21st position.
In the early stages it was Romain Grosjean who had fast race pace and on lap 7 he again overtook using DRS, this time Hamilton was his victim.
Button complained on the radio about his rear tyres losing performance while the Lotus looked very strong as Räikkönen again put the DRS to good use and claimed Alonso on the 9th lap for 5th position.
Alonso, Rosberg, Massa and Pérez rounded out the top 10 while 7 time world champion Michael Schumacher was in 13th – still clawing his way back into points contention.
During the same lap, Maldonando used DRS to put a move on Pérez, however went deep and the two duelled to turn 4 when di Resta who was behind them pounced through the inside as they battled each wide of the apex.
It appeared the Lotus' were equally matched and Räikkönen was starting to lose grip from either following the dirty air of his teammate or his tyres were hitting the 'cliff' (performance-wise) or both.
The two Lotus cars were next to cross the line with Räikkönen (2nd) achieving his first podium since the 2009 Italian Grand Prix where he drove for Scuderia Ferrari.
Red Bull teammate Mark Webber finished 4th for the fourth consecutive time this season leaving him as clearly the most consistent driver of the 2012 championship so far.
Di Resta managed to hold off the Ferrari of Alonso by less than 0.3 of a second and made his two-stop strategy work effectively to claim 6th place and equal his best ever Formula One result (2011 Singapore Grand Prix).
[45] Hamilton, who lost around fifteen seconds through wasted pit stop time, was a disappointing 8th; while behind him Felipe Massa picked up his first points of the year by finishing 9th.