The actor sported heavy prosthetics to take on the role of the comic book villain.
He could also be seen having his make-up touched up during filming for the blockbuster.
Farrell appeared to be wearing a wig with a receding hairline, as well as a false nose and scars on his cheek.
He was dressed in a dark suit and leather coat as he filmed scenes with Pattinson as Bruce Wayne and John Turturro as Carmine Falcone.
Farrell could also be seen using a clear face shield in between takes, as extras and members of the crew wore face coverings.
Production on the film began in Glasgow earlier this year, but was halted due to the pandemic.
It resumed months later but was suspended again as a precaution against coronavirus.
Filming continues in Liverpool after the Prime Minister launched the three-tier system of local alert levels for England on Monday, with the Liverpool city region placed in the most serious “very high” risk category from Wednesday.
A Liverpool City Council spokeswoman told the PA news agency: “The new restrictions in Liverpool do not currently impact on filming in the city region.
“The Film Office is working closely with every single production to ensure Covid-safe measures are in place and are being adhered to in accordance with rigorous industry protocols.”
The Batman, which is directed by Matt Reeves, will see Pattinson, 34, follow in the footsteps of actors including Christian Bale, Ben Affleck, Val Kilmer, Michael Keaton and George Clooney in playing the Dark Knight.
The film also stars Zoe Kravitz as Catwoman, Andy Serkis as Alfred Pennyworth and Jeffrey Wright as Gotham City’s police chief Commissioner Gordon.
