The Jaguar driver topped the timesheets at the end of the four-and-a-half-hour session with a 1m24.791s, leaving him just 0.023s clear of Porsche's Antonio Felix da Costa.
The same pair also topped the standings on Tuesday morning prior to a fire in the garage of battery supplier WAE (formerly known as Williams Advanced Engineering) which halted proceedings at the Circuit Ricardo Tormo in Spain.
With the FIA conducting an investigation and satisfied with the findings, running once again resumed on Thursday at 2pm local time.
Edoardo Mortara set the early pace with a 1m25.661s as Mahindra ran only one car after the team suffered damage as a result of the blaze on Tuesday, including to the car of Nyck de Vries.
It meant the ex-AlphaTauri Formula 1 driver was unable to take part in the session having finished last of the runners on Tuesday morning, his first time driving Mahindra's Gen3 machine.
Mortara finished Thursday's session third overall, just 0.112s behind Evans, but came to a stop twice on the same lap before recovering to the pits with over an hour left on the clock.
Robin Frijns, on his return to Envision, was the only other driver to dip below the 1m25s mark in fourth.
Porsche's Pascal Wehrlein finished fifth with a 1m25.004s, but came to a stop on track in the final minutes, which prompted a red flag and early end to the session.
Maximilian Guenther (Maserati MSG), Oliver Rowland (Nissan), Norman Nato (Andretti Global), Jehan Daruvala (Maserati MSG) and Nick Cassidy (Jaguar) completed the top 10.
Reigning champion Jake Dennis finished 12th, just over four tenths off the pace, the Briton driving the car for the first time as his seat was taken by nominated rookie Zane Maloney on Tuesday morning.
Given the limited running, most teams opted to run their full-time drivers in the session, with only Porsche deciding to run a rookie – Gabriela Jilkova was given some track time before handing over to da Costa.
ERT drivers Dan Ticktum and Sergio Sette Camara occupied the bottom of the timesheets, with the latter completing only eight laps due to a battery issue which hindered the Brazilian's running.
In comparison, the most laps in the session were completed by Envision's Sebastien Buemi, who hit 75 laps down in 17th, less than half a second off the pace.
In the final 12 minutes, Evans set a new session best in the first sector before backing off over the remainder of the lap, leaving his 1m24.791s as the benchmark and three tenths off his best from Tuesday.
Friday's running is expected to be held between 8:30am and 6:30pm, which will mean only half an hour will have been lost from the original schedule prior to the fire.
