The majority of teams dedicated the afternoon to the first full-race simulations of 2013, meaning that the morning order was largely unchanged.
It also meant Alonso, who eventually worked his way down to a 1m21.875s before lunch, stayed on top for the remainder of the third day in Catalunya.
His time is the fastest seen so far at Barcelona and almost half a second quicker than the corresponding soft-compound best of 2012 winter testing at the track.
As was the case in the morning, Nico Hulkenberg and Romain Grosjean occupied second and third respectively, both within four tenths of a second of Alonso's time.
Grosjean was the first of the day's runners to complete a full race simulation, which included four pitstops.
Thanks largely to that stint he also ended as Thursday's busiest driver on 119 laps.
Others ran long-race simulations of their own, although some were interrupted when Giedo van der Garde's Caterham stopped on the Turn 3 entry 15 minutes before the session's end.
Van der Garde had been one of the afternoon's few improvers, and had just set his best time - a low 1m26s - before causing the stoppage.
Max Chilton also improved in the Marussia, while Valtteri Bottas, taking over from Pastor Maldonado in the FW35, ended the day sixth, fractions of a second behind his team-mate.
Jenson Button, Adrian Sutil, Mark Webber and Jean-Eric Vergne occupied seventh through to 10th, just as they did at the close of the morning.
Both Webber and and Vergne broke into triple figures on the lap count.
Sutil meanwhile will hand over to Force India's 2012 reserve driver Jules Bianchi, his main rival for a 2013 drive with the team, for the final day tomorrow.
1. Fernando Alonso - Ferrari - 1:21.875 - 97 laps
2. Nico Hulkenberg - Sauber - 1:22.160 - +0.285 - 91
3. Romain Grosjean - Lotus - 1:22.188 - +0.313 - 119
4. Nico Rosberg - Mercedes - 1:22.611 - +0.736 - 108
5. Pastor Maldonado - Williams - 1:22.675 - +0.800 - 79
6. Valtteri Bottas - Williams - 1:22.826 - +0.951 - 68
7. Jenson Button - McLaren - 1:22.840 - +0.965 - 71
8. Adrian Sutil - Force India - 1:22.877 - +1.002 - 78
9. Mark Webber - Red Bull - 1:23.024 - +1.149 - 108
10. Jean-Eric Vergne - Toro Rosso - 1:23.366 - +1.491 - 106
11. Max Chilton - Marussia - 1:25.690 - +3.815 - 58
12. Giedo van der Garde - Caterham - 1:26.17s - +4.302 - 83