For the first time in his 200-race career Alonso faces being out-qualified by a team-mate for a fifth consecutive grand prix.
After Felipe Massa posted the quickest lap over Friday's two 90-minute practice sessions at the Sepang International Circuit, the double world champion on Saturday edged his Ferrari team-mate.
In the final hour-long run ahead of qualifying the duo finished one-two, with Alonso posting a time of one minute 35.391secs, finishing 0.622secs clear of Massa.
That was 0.051secs down compared to the Brazilian's time on Friday, and with a reason for the disparity on Saturday.
Over the first two sectors, with Alonso following behind Massa by around 300 metres or so, the pairing matched each other stride for stride and on time.
In the final sector, however, Massa had to slow slightly as he came up on Force India's Adrian Sutil, whilst Alonso had a clear run to the line to ultimately finish comfortably clear.
Behind the Ferraris was Lewis Hamilton in his Mercedes, the Briton quickest on the medium compound before the field switched to the faster soft Pirelli tyre over the final 20 minutes.
Hamilton finished just 0.052secs behind Massa, and just over two tenths of a second ahead of Red Bull's reigning three-times world champion Sebastian Vettel who was fourth quickest.
So far it has been difficult to determine whether Red Bull have showed their hand and whether Vettel has a genuine shot at a third successive pole position to start this season.
Vettel was up on team-mate Mark Webber by just over a tenth of a second, with the Australian fifth on the timesheet and a second down on Alonso.
Sutil was a strong sixth, two seconds ahead of 16th-placed team-mate Paul Di Resta, although the Briton failed to get a clear lap on his set of softs.
Kimi Raikkonen, winner of the season-opening Australian Grand Prix, was seventh ahead of McLaren pair Jenson Button and Sergio Perez.
Despite many updates to the car to get them closer to the leaders after a dismal start to their campaign, there are still issues to overcome.
At least Perez avoided any incidents in the session after Friday's damaging his front wing in FP1 and his rear in FP2 with runs over the gravel and into tyre walls.
Sauber's Nico Hulkenberg completed the top 10, but almost 1.5secs behind Alonso, with the Toro Rossos of Jean-Eric Vergne and Daniel Ricciardo faring well in 12th and 13th.
After issues on Friday with his Marussia that restricted his second session to just five laps, Max Chilton managed 16 laps on Saturday and was 21st, albeit 1.1secs behind 19th-placed team-mate Jules Bianchi.