Alonso, third overall in the championship, clocked 1 minute, 18.482 seconds. Hamilton was .419 seconds behind, and Sebastian Vettel .535 behind for Red Bull. Frenchman Jean-Eric Vergne was fourth best for Toro Rosso.
Spectators waited for nearly 40 minutes as drivers stayed in their garages until the track dried after some showers.
There is a final practice session on Saturday morning before qualifying in the afternoon.
“It felt really good out there today. I had a good first session and was then really pleased to get those last few laps in the dry this afternoon,” Hamilton said. “I’m feeling pretty set for Saturday. There is still some work to do, but we have tomorrow to look into that.”
The British driver is confident he can end his barren run in Monaco, where he has not won since 2008, the year he won the F1 title.
“This track is one of the coolest ever,” Hamilton said. “It’s such a classic race, and I’ve been trying to win here again since 2008, so I’m hoping this is the year as we have such a great car.”
“It seems that we are looking very quick here again, although our main competitors seem to be a little closer to us than in Barcelona,” the German said. “The conditions weren’t great this afternoon so I didn’t take any risks as there was nothing to learn on the wet parts of the track.”
Monaco’s tight, sinewy circuit makes overtaking almost impossible and puts whoever gets pole into a prime position.