For Lewis Hamilton, the hour-long run ended in dramatic fashion with a rear-left suspension failure that will keep his Mercedes crew busy in the run up to qualifying later on Saturday.
As for Alonso, on the back of his 31st-career victory in China last Sunday, he has been highly impressive around the desert-based Bahrain International Circuit.
With a high police presence around the track as local authorities are determined to keep anti-government protesters at bay, Formula One is virtually oblivious to what goes on away from it.
On the circuit, Alonso led a tightly-bunched field, with the top six separated by just two tenths of a second, and the front nine by half a second.
Alonso, last on pole in Germany last year, set a lap of one minute 33.247secs which was almost a second quicker than the leading time of Saturday posted by Lotus' Kimi Raikkonen.
As in second practice, the Red Bull drivers had to settle for second and third on the timesheet, on this occasion with reigning world champion Sebastian Vettel ahead of Mark Webber.
Vettel, who finished 0.101secs behind Alonso and 0.032secs ahead of team-mate Webber, had looked poised to snatch top spot from Alonso as he posted personal best times in the first two sectors, only to be blocked by a Caterham.
Raikkonen was down in fourth, 0.199secs adrift, with Hamilton an improved fifth and 0.208secs down after complaining of balance issues on Saturday.
Mercedes and Hamilton, however, have far more to worry about now in the wake of his rear-suspension giving way on his in-lap just after the session had expired.
Behind the 28-year-old were Lotus' Romain Grosjean, appearing more comfortable with the new chassis given to him this weekend, followed by Force India pair Adrian Sutil and Paul Di Resta.
Mercedes' Nico Hulkenberg was ninth quickest, 0.517secs off Alonso's pace, with Sauber's Nico Hulkenberg completing the top 10.
Felipe Massa inexplicably now finds himself struggling for pace as the Brazilian, quickest in first practice, was languishing in 11th at the end of FP3 and 0.702secs behind team-mate Alonso.
As for McLaren, their struggles continue with Jenson Button and Sergio Perez 12th and 13th, the latter a full second behind Alonso.
Towards the rear, Marussia also face issues as Max Chilton managed just seven laps due to the team having to replace the KERS water pump.
Chilton, however, was not last as that position belonged to Sauber's Esteban Gutierrez who concentrated on a long run, completing 28 laps overall, but finishing 6.345secs down.
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