The Argentinian posted a 1m42.857s lap to outpace teammate Kazuki Nakajima's 1m44.004s in the sister #8 Toyota TS050 Hybrid.
The gap of just over a second was more than double the 0.54s performance advantage held by the #7 car Lopez shares with Kamui Kobayashi and Mike Conway under the success handicap system.
The two Toyotas put in their quick laps right at the start of the 90-minute Friday morning session: Lopez recorded his time on his first flying lap and Nakajima on his fourth.
Racing Team Nederland headed the LMP2 times in the second of the trio of free practice sessions ahead of qualifying on Friday evening.
Nyck de Vries recorded a 1m49.601s right at the start of the session in the team's TDS Racing-run Oreca 07 to end up more than a second and a half quicker than the Signatech Alpine Oreca.
A 1m50.302s from Pierre Ragues put Signatech Alpine a tenth ahead of United Autosports driver Phil Hanson's 1m50.407s.
Will Stevens took fourth in class with a 1m50.854s aboard the JOTA Sport-run Jackie Chan DC racing Oreca.
Ferrari jumped to the front of the GTE Pro order after bringing up the rear in the first period of free practice on Thursday.
Miguel Molina topped the class times with a 1m57.193s in the #71 Ferrari 488 GTE Evo, which put him just over two tenths up on Porsche driver Gianmaria Bruni on a 1m57.442s.
The second Ferrari was a further four tenths back in Daniel Serra's hands with a 1m57.801s.
Aston Martin, which was quickest in class on Thursday, took fourth with a 1m57.900s from COVID-stricken Alex Lynn's stand-in Richard Westbrook in the best of its Vantage GTEs.
The second Porsche 911 RSR took fifth in Kevin Estre's hands ahead of Nicki Thiim's #95 Aston.
GTE Am was led by the Dempsey Proton Porsche in which series debutante Jaxon Evans posted a 1m57.773s. The fastest of the Project 1 Porsche 911 RSRs was second with a 1m58.889s from Jeroen Bleekemolen.
FP2 results:
| Cla | # | Drivers | Car | Class | Laps | Time | Gap |
|---|---|---|---|---|---|---|---|
| 1 | 7 | Toyota TS050 Hybrid | LMP1 | 40 | 1'42.857 | ||
| 2 | 8 | Toyota TS050 Hybrid | LMP1 | 34 | 1'44.004 | 1.147 | |
| 3 | 29 | Oreca 07 | LMP2 | 38 | 1'48.601 | 5.744 | |
| 4 | 36 | Alpine A470 | LMP2 | 41 | 1'50.302 | 7.445 | |
| 5 | 22 | Oreca 07 | LMP2 | 30 | 1'50.407 | 7.550 | |
| 6 | 37 | Oreca 07 | LMP2 | 41 | 1'50.854 | 7.997 | |
| 7 | 38 | Oreca 07 | LMP2 | 41 | 1'51.153 | 8.296 | |
| 8 | 47 | Dallara P217 | LMP2 | 31 | 1'51.688 | 8.831 | |
| 9 | 71 | Ferrari 488 GTE EVO | LMGTE PRO | 34 | 1'57.193 | 14.336 | |
| 10 | 91 | Porsche 911 RSR - 19 | LMGTE PRO | 35 | 1'57.422 | 14.565 | |
| 11 | 88 |  Khaled Al Qubaisi Jaxon Evans Marco Holzer | Porsche 911 RSR | LMGTE AM | 40 | 1'57.773 | 14.916 |
| 12 | 51 | Ferrari 488 GTE EVO | LMGTE PRO | 36 | 1'57.801 | 14.944 | |
| 13 | 57 | Porsche 911 RSR | LMGTE AM | 37 | 1'57.889 | 15.032 | |
| 14 | 97 | Aston Martin Vantage AMR | LMGTE PRO | 40 | 1'57.900 | 15.043 | |
| 15 | 92 | Porsche 911 RSR - 19 | LMGTE PRO | 36 | 1'58.030 | 15.173 | |
| 16 | 56 | Porsche 911 RSR | LMGTE AM | 36 | 1'58.205 | 15.348 | |
| 17 | 54 | Ferrari 488 GTE EVO | LMGTE AM | 35 | 1'58.475 | 15.618 | |
| 18 | 95 | Aston Martin Vantage AMR | LMGTE PRO | 37 | 1'59.070 | 16.213 | |
| 19 | 62 | Ferrari 488 GTE EVO | LMGTE AM | 38 | 1'59.095 | 16.238 | |
| 20 | 77 | Porsche 911 RSR | LMGTE AM | 32 | 1'59.408 | 16.551 | |
| 21 | 98 | Aston Martin Vantage AMR | LMGTE AM | 40 | 1'59.504 | 16.647 | |
| 22 | 86 | Porsche 911 RSR | LMGTE AM | 31 | 1'59.689 | 16.832 | |
| 23 | 90 | Aston Martin Vantage AMR | LMGTE AM | 38 | 1'59.696 | 16.839 | |
| 24 | 83 | Ferrari 488 GTE EVO | LMGTE AM | 35 | 2'00.418 | 17.561 | |
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