The current drivers’ championship leader clocked a lap of the Hockenheim circuit in one minute 16.24 seconds towards the end of the session edging out rival and former team-mate Lewis Hamilton of McLaren.
Alonso had looked strong throughout the session and shortly after a new front wing design was fitted to his car the Spaniard leapt to the top of the leaderboards, eclipsing the Englishman’s time by 0.77 seconds.
Sauber driver Mexican Sergio Perez was third fastest ahead of Finn Kimi Raikkonen of Lotus.
Red Bull duo Australian Mark Webber and German Sebastian Vettel were fifth and sixth fastest respectively ahead of the controversial Venezuelan Pastor Maldonado of Williams.
Brazilian Felipe Massa was eighth quickest in the second Ferrari followed by Japanese Kamui Kobayashi in the second Sauber.
Frenchman Romain Grosjean was tenth fastest in the other Lotus.