Alonso's time of one minute 13.307 seconds came in the early afternoon
By Sarah Holt
BBC Sport in Valencia
Fernando Alonso laid down a marker for Ferrari by setting the fastest time so far in winter testing.
The Spaniard clocked one minute 13.307 seconds in Valencia as he improved on world champion Sebastian Vettel's speed for Red Bull by 0.3secs.
Scot Paul di Resta finished just over half a second behind Alonso in last year's Force India.
Lewis Hamilton made his first appearance in testing in the 2010 McLaren and finished fourth overall.
Alonso's time came in the early afternoon, after he spent much of the morning working on the aerodynamic development of the 2011 Ferrari before carrying out comparison tests between various types of Pirelli tyres.
During a sequence of quicker laps the Spaniard, who finished runner-up to Vettel in last season's championship, unleashed two laps faster than Vettel's best to replace the world champion at the top of the timesheets.
"I am happy with the work we did today," said Alonso.
"Yesterday we concentrated mainly on the systems on the car, on checking that everything was OK, while on this second day we were able to go deeper into our understanding of its behaviour, even with different fuel loads, making the first changes to the set-up. For example, we tried to deal with the oversteer and to find ways of dealing with tyre degradation over a long distance.
"From the reliability point of view, this is definitely a good start. The F150 proved to be very strong and we can be happy about that. As to whether we will be competitive, we won't really know for sure until Bahrain."
Mark Webber had his first taste of the Red Bull with less than an hour left on the clock, but a late red flag hampered his progress and he was only the 14th fastest driver of the day, four seconds behind Alonso.
Australian Webber said: "I didn't get so long in the car today, so we will start the real work tomorrow. There was a bit of a problem with the installation, something with the pedals, so it took a bit longer than we expected.
"It wasn't the smoothest day, but we're back tomorrow - it's great that the guys have got the car here for the first test and I'm looking forward to driving it more."
Hamilton had to settle for a day in the 2010 McLaren as he re-entered the fray. The team said they were focused on understanding more about the Pirelli tyres, which will be used this season instead of Bridgestone.
"It feels great to get back in the car," said the Englishman. "It was good to brush off the cobwebs and straight away I felt at home and it was quite a productive day.
"We tried to replicate the 2011 downforce levels but it was not 100% accurate [as a 2010 car] but got a good understanding of the tyres and we covered quite a lot.
"The tyres are easier to feel, there's not as much grip as there is on the Bridgestones so they are a little bit harder to control over a longer stint but everyone is in the same boat.
"I'm looking forward to driving the new car next week."
McLaren take the wraps off their 2011 car in Berlin on Friday ahead of next week's Jerez test.
Mercedes returned to the track after hydraulics problems halted their progress on day one, with Nico Rosberg replacing Michael Schumacher at the wheel.
Rosberg, who was waylaid by another stop on track, finished seventh with a best time of 1:14.645, just behind Hispania's Narain Karthikeyan (1:14.472).
The morning session saw Rosberg's team try out the returning Kers energy recovery system for the first time. The Mercedes unit was widely thought to be the most efficient Kers unit when it was first introduced in 2009 and the team said it was "going well".
Schumacher will be back in the car on Thursday but the seven-time world champion was at the Ricardo Tormo circuit to keep an eye on progress.
Robert Kubica finished fifth fastest for Renault on his first day in the team's new car.
Renault have attracted a lot of attention in Valencia by opting for an innovative design concept which sees the exhaust exit through the front of the sidepods of their car.
The design of the new Williams, particularly its neatly packaged rear, has also drawn praise but Rubens Barrichello said the team were still understanding their new challenger.
The Brazilian caused the first red flag of day two when he stopped his car on the far side of the track with an electrical problem.
He said: "We learnt a lot. It was all positive; the only drawback from the day is that the number of buttons on the steering wheel can distract you from the driving.
"I feel optimistic but it's early days and we are still playing catch-up."
Venezuelan Pastor Maldonado took over driving the Williams in the afternoon and will stay at the helm on the final day.
Di Resta also caused a red flag as he had a spin on worn tyres but otherwise the Scot had a successful session collecting data as Force India prepare to launch their 2011 car in Jerez.
Formula 1 pre-season test, Valencia, day two:
1. Fernando Alonso (Ita) Ferrari one minute 13.307 seconds
2. Sebastian Vettel (Ger) Red Bull-Renault 1:13.614s
3. Paul di Resta* (GB) Force India-Mercedes 1:13.844s
4. Lewis Hamilton* (GB) McLaren-Mercedes 1:14.353s
5. Robert Kubica (Pol) Renault 1:14.412s
6. Nico Rosberg (Ger) Mercedes 1:14.645s
7. Timo Glock* (Ger) Virgin-Cosworth 1:15.408s
8. Rubens Barrichello (Brz) Williams-Cosworth 1:16.023s
9. Sergio Perez (Mex) Sauber-Ferrari 1:16.198s
10. Pastor Maldonado (Ven) Williams-Cosworth 1:16.266s
11. Sebastien Buemi (Swi) Toro Rosso-Ferrari 1:16.359s
12. Jaime Alguersuari (Spa) Toro Rosso-Ferrari 1:16.474s
13. Mark Webber (Aus) Red Bull-Renault 1:17.365s
14. Narain Karthikeyan* (Ind) Hispania-Cosworth 1:17.769s
15. Heikki Kovalainen (Fin) Lotus-Renault 1:20.649s
* 2010 car