Hamilton, hoping for a better weekend after being hampered by a suspension problem in Japan and then misguidedly criticising team-mate Jenson Button on Twitter, produced a lap of one minute 39.148 seconds late in the session to edge out Alonso by three tenths of a second.
The Spaniard came to Korea on the back foot, after seeing his title lead dramatically cut to just four points by Sebastian Vettel in Japan last weekend.
But with Ferrari having brought some new pieces to Korea they looked a more competitive proposition than at recent rounds as Alonso topped the times for most of the session before being usurped by Hamilton.
With the Korea International Circuit barely used outside of the F1 race weekend, the majority of teams chose to wait for the dusty surface to be cleaned up before venturing out to post any competitive lap times.
Red Bull waited until the halfway-point of the 90-minute session before posting a time. Mark Webber was third fastest while team-mate Vettel was fifth as the team assessed the performance of the soft compound tyre rather than seeking ultimate pace.
There was a moment of concern for team boss Christian Horner during the dying seconds as Webber considered diving up the inside of his team-mate in the final sector, but thought better of it as the German closed the door.
Felipe Massa, fresh from his first podium in two years, underlined Ferrari's encouraging start by separating the two Red Bulls in fourth.
Michael Schumacher and Nico Rosberg were sixth and seventh for Mercedes with Romain Grosjean and Paul Di Resta next up.
Button had topped the timesheets early on in the second McLaren, but faded to 10th by the end of the session.
Grosjean and Lotus team-mate Kimi Raikkonen were running a new exhaust system but the Finn's championship aspirations appear to be ever-diminishing as he was back in 11th.
Pastor Maldonado was 12th while Kamui Kobayashi, the podium hero in Japan, was 14th, just ahead of Sauber team-mate Sergio Perez.
Jules Bianchi, stepping in for Nico Hulkenberg at Force India, was the quickest of the four drivers given an outing in this morning's session.
He was 13th, with Valtteri Bottas 18th for Williams, Giedo van der Garde 22nd for Caterham and Dani Clos last for HRT, some 6.5 seconds off Hamilton's time, and 1.2 seconds slower than team-mate Pedro de la Rosa.