The German, who is under evaluation with the Enstone-based team as a possible replacement for the injured Robert Kubica, is all but assured of replacing his former BMW Sauber team-mate after a stunning time of 1:20.361 late in the afternoon.
HeidfeldÃ¢â‚¬â„¢s lap sees Renault return to the top of the time sheets after Kubica finished the first test in Valencia on top before crashing in the Ronde di Andora rally on Sunday.
Alonso ran over 500km in the F150th Italia, concentrating on long runs with a heavy fuel load as the car passed 1500km of testing.
The 29-year-old delighted the large gathering of Spanish fans who had turned up to watch him by topping the time sheet for much of the day, but finished one tenth slower than Heidfeld when the chequered flag came down.
Michael Schumacher was third quickest for Mercedes after topping the time sheets on day two as the W02 again showed good pace for much of the day, the seven-time champion was half a second slower than Alonso with a 1:20.054.
Lewis Hamilton spent much of the day in the garage as McLaren waited for new parts to arrive limiting the 2008 world champion to just 36 laps.
With a number of short stints he nevertheless managed to snatch fourth place, seven tenths off the pace, and just four hundredths slower then Schumacher.
It was an eventful day for SauberÃ¢â‚¬â„¢s Kamui Kobayashi who eventually finished fifth quickestÃ¢â‚¬â€just eight tenths off the paceÃ¢â‚¬â€despite twice causing red flags to come out after parking his car off the track following mechanical issues.
World champion Sebastian Vettel was able to match AlonsoÃ¢â‚¬â„¢s pace in the afternoon but it was clear the team were sandbagging as they ran through a number of performance programmes, eventually finishing sixth quickest with a time of 1m21.574.
Toro RossoÃ¢â‚¬â„¢s SÃƒÂ©bastien Buemi was seventh quickest, and was another driver who brought out the red flags this time just 10 minutes before the end of the session, but the Swiss driver will be happy to have finished just one tenth slower than Vettel.
Heikki Kovalainen was eighth quickest for Team Lotus, with a time of 1:21.711, 1.3 seconds slower than Heidfeld on a memorable day for the Anglo-Malaysian team.
Williams again suffered technical problem with KERS on the FW33 limiting the carÃ¢â‚¬â„¢s performance as Rubens Barrichello completed 99 laps but could only finish ninth with a 1:22.227.
Paul di Rest suffered early on with brake problems and was tenth for Force India with a time of 1:22.945 after his first outing in the VJM04. He spun later in the day at the Curva Angel Nieto to bring out the red flags.
JÃƒÂ©rÃƒÂ´me dÃ¢â‚¬â„¢Ambrosio was by far the slowest driver on track and was eleventh quickest, 2.5 seconds adrift of di Resta at the bottom of the time sheets as he completed 72 laps in the MVR-02.
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BIOGRAPHY: Ethan Hazard
BIOGRAPHY: Daniel Sturridge