Bourdais posted a 1m34.732s to head the times 15 minutes from the end of the one-hour session, eclipsing his 1m34.949s that put the #01 Cadillac DPi-V.R at top of the timesheets early in another session affected by rain.
The track was slightly damp when the green flag was waved and there were further spots of rain mid-session, but times were coming down when the session was red-flagged with just under 10 minutes remaining.
The session yielded the first representative times of the week ahead of a race that will be held in dry but cold conditions according to weather forecasts.
Bourdais’s lap compared with the fastest practice lap of 1m34.351s from last weekend’s pre-race Roar test and the 1m34.034s that gave JDC-Miller driver Tristan Vautier pole position for the grid-setting 100-mile qualifying race
Loic Duval had just gone second in the JDC-Miller Caddy when the interruption came, the Frenchman posting a 1m35.095s.
Jose Maria Lopez ended up third fastest quickest in the best of the Action Express Racing Cadillacs with a 1m35.235.
Earl Bamber took fourth with a 1m35.587s in the second Ganassi car and Action Express driver Pipo Derani fifth with a 1m35.959s as Cadillac locked out the top five positions.
The two Acuras jumped up the order straight after the session restarted with five minutes left on the clock.
A 1m36.049s from Alex Rossi put the Wayne Taylor Racing Acrua ARX-05 sixth, while Tom Blomqvist improved to 1m36.347s to end up seventh.
The late run from the Acuras demoted Phil Hanson in the fastest of the LMP2s to eighth position overall. The Briton’s 1m37.639s in the United Autosports Oreca put him just five hundredths ahead of Ferdinand Habsburg’s 1m37.689s in the Tower Motorsport entry.
Harry Tincknell was a further two tenths back and third in class in the PR1/Mathiasen Oreca.
Mirko Bortolotti led the GT Daytona Pro field in his TR3 Racing Lamborghini Huracan GT3 Evo. The Italian’s 1m46.085s put him two tenths up on Matteo Cairoli’s 1m46.334s in the Proton-run WeatherTech Racing Porsche 911 GT3 R.
Jack Hawksworth took third in the best of the Vasser Sullivan Lexus R CF GT3s. The Briton’s 1m46.372s was just a couple of hundredths faster than Jan Heylen managed in the Wright Motorsports Porsche to head the GTD pro-am class times.
Andretti Autosport led the way in LMP3, Rasmus Lindh’s 1m44.015s in his Ligier JS P320 giving him nearly a half-second margin on Moritz Kranz in the fastest of the Muehlner Motorsport Duqueine D08.
The session was the final time the 61-car field will take to the track ahead of the race, which starts at 1:40pm local (Eastern) time on Saturday.