Three weeks after the controversial Bahrain Grand Prix, Vettel of Red Bull led the way for much of the session before Spaniard Alonso, a two-time champion, clocked his best lap of one minute and 24.430 seconds to outpace him by less than one-tenth of a second.
Japanese Kamui Kobayashi of Sauber was third fastest ahead of Briton Jenson Button, the 2009 champion, in his McLaren, running with a new raised nose on his car as the British team evaluated new ideas to improve their race performances.
Finnish rookie Valtteri Bottas, the Williams team's reserve and test driver, was fifth quickest ahead of German Michael Schumacher, 43, the seven-time champion, maintaining the competitive form of the Mercedes team this year.
Frenchman Romain Grosjean was seventh for Renault, ahead of Briton Lewis Hamilton, the 2008 champion, in the second McLaren, running his car with the lower nose configuration.
Finn Kimi Raikkonen, the 2007 champion, was ninth fastest for Renault ahead of German Nico Hulkenberg of Force India.
Brazilian Felipe Massa was down in 12th in the second Ferrari ahead of Australian Mark Webber in the second Red Bull with German Nico Rosberg 14th in the second Mercedes.
On a dry, bright and warm morning at the Circuit de Catalunya, the field were closely packed as they tested and developed new parts for their revamped cars ahead of the opening race of the European part of the 2012 season.
Alonso's performance in the closing stages suggested that Ferrari may have either found a small performance breakthrough or run with a lighter fuel load to appease their fans - and locals supporting Alonso back on Spanish soil.
Bottas was the fastest of the rookie reserve drivers in action, way ahead of the nearest rival in that category, Frenchman Jules Bianchi, who was 18th for Force India, American Alex Rossi, who was 19th for Caterham and local boy Spaniard Dani Clos who was 24th and last, a full 2.5 seconds slower than his compatriot and Hispania team-mate Pedro de la Rosa.
Top 10 Fastest times:
1. Fernando Alonso (ESP/Ferrari 1:24.430,
2. Sebastian Vettel (GER/Red Bull) 1:24.808,
3. Kamui Kobayashi (JPN/Sauber 1:24.912,
4. Jenson Button (GBR/McLaren Mercedes) 1:24.996,
5. Valtteri Bottas (FIN/Williams 1:25.120,
6. Michael Schumacher (GER/Mercedes AMG 1:25.187,
7. Romain Grosjean (FRA/Lotus) 1:25.217,
8. Lewis Hamilton (GBR/McLaren Mercedes) 1:25.252,
9. Kimi Raikkonen (FIN/Lotus) 1:25.285,
10. Nico Huelkenberg (GER/Force India-Mercedes) 1:25.339