Porsche's lap time was 3m 19.71s with a top speed of 245.7km, while the best Toyota LMP1 team got across the line in 3m 18.793s, with a top speed of 246.8km on the Circuit de la Sarthe.
"Driving the 919 at night is incredible. P3 so far in qualifying," Bamber told supporters on Twitter.
"Working on the race pace. It's going to be a hot, quick race."
Earlier at the official test day on June 5, Bamber set the quickest lap time by a Porsche in 3m 21.512s, which was the fifth best time of the day.
Live coverage of The 24 Hours of Le Mans race begins early on Sunday morning at 12.30am on Sky Sport Pop-up 4 (Channel 58) and will cover the entire race from start to finish.
Racing starts from 1am.