Although the tail end of Hurricane Lorenzo failed to bring the extreme weather predicted, steady rain made the gravel tracks in the Snowdonia mountains extremely slippery and grip was at a premium all morning.
Thierry Neuville, the third driver in the title battle, ended fourth in his Hyundai i20, 4.8sec behind Meeke. The Belgian had no major problems but a tyre selection mix-up at mid-leg service cost valuable seconds this afternoon.
Team-mates Andreas Mikkelsen and Craig Breen completed the top six, half a minute off the lead.
Latvala ran as high as third before rolling his Yaris heavily and he will not restart tomorrow. Lappi slid his C3 into a ditch and could not regain the track.