Vettel, the reigning triple world champion and current title leader, took full advantage of the warm, dry conditions for FP2 to edge Alonso by just 0.017secs at Barcelona's Circuit de Catalunya.
Alonso spearheaded a one-two after the initial 90-minute session to the delight of his Spanish fans, although conditions were far from ideal.
Steady rain fell prior to the start, turning to drizzle in the early stages, and forced the intermediate tyres to be used for those who bothered to venture out.
The rain eventually relented to offer up a dry-ish line late on and allow the teams to switch to the hard tyre, resulting in considerable improvement in the closing stages.
Alonso ultimately held sway to top the timesheet with a lap of one minute 25.252secs, but on a dry track come the start of the FP2, that was eclipsed almost immediately.
On the medium Pirelli compound, the faster of the two being used for this weekend, Vettel led the way with a 1:22.808secs, with Alonso hot on his heels.
Vettel's Red Bull team-mate Mark Webber was also in close attendance as the 36-year-old Australian was only 0.083secs off the pace.
But there is more to come because to put the times into perspective, come the conclusion to the eight days of testing at this track in late February and early March, Nico Rosberg in his Mercedes was quickest with a 1:20.130secs.
At least the teams were finally able to put the upgrade packages on their cars - as they traditionally possess when the racing returns to Europe - through their paces after failing to gain too many clues from the rain-hit morning session.
With so many new parts on the McLarens, Jenson Button and Sergio Perez managed just six laps apiece in FP1, in contrast to every other driver who achieved double figures.
That was primarily due to the fact with pressure sensors on the car to determine the performance of the parts, they could not run for fear of them filling with water and being unable to operate.
In a dry FP2, Button and Perez managed 35 and 31 laps respectively as McLaren ran through a number of programmes.
But their times still made for grim reading as Button was 12th and Perez 13th, 1.5secs and two seconds behind Vettel.
Off the leading trio by two tenths of a second was Kimi Raikkonen in his Lotus, bidding to become the first man to win three times at this circuit with different teams after previous triumphs with McLaren and Ferrari.
Ferrari's Felipe Massa was fifth quickest, followed by Lewis Hamilton who repeated his sixth place from the morning, with the 28-year-old 0.332secs off the pace, with Rosberg seventh and 0.590secs down.
Force India duo Adrian Sutil and Paul Di Resta were eighth and 10th, sandwiching Toro Rosso's Jean-Eric Vergne, with all three just over a second down.
Di Resta's session, however, ended 18 minutes early as he strangely lost the tread on his left-rear tyre coming out of the final corner.
After Pirelli's issues with blown rubber in China where Hamilton and Massa suffered, but with debris attributed as the cause, this latest incident was somewhat different.
After making way in FP1 for reserve Rodolfo Gonzalez, Max Chilton's run in FP2 saw him clock 26 laps in his Marussia, but finishing four seconds adrift of Vettel at the bottom of the timesheet.