Toyota had seemed set to return to the top of the Le Mans timesheets for the first time since opening practice on Wednesday, with Kamui Kobayashi heading the majority of the session.
However, a late 3m26.579s from Antonio Fuoco in the #50 499P LMH smashed Kobayashi's best by almost a second.
And, with eight minutes to go, Alessandro Pier Guidi set a 3m27.013s lap to go second, despite the #51 Ferrari having spent the first half of the three-hour session in the pits.
The Toyota GR010 HYBRIDs were denied the chance to respond as a late full-course yellow, when Manuel Maldonado went off, hampered any further late improvements. Instead, Kobayashi had to settle for third in the #7 Toyota.
Mathieu Jaminet in the #75 Porsche 963 LMDh was the initial pacesetter on a 3m28.454s but was soon usurped by the two Toyotas.
Kobayashi claimed top spot with a 3m27.822s in the #7 car, before Sebastien Buemi went second in the sister #8 machine on 3m27.879s.
However, Kobayashi then improved to a 3m27.580s that looked set to be the benchmark for the remainder of third practice until the late Ferrari efforts.
Source: Autosport