Leclerc had set the fastest lap in the first practice session at Yas Marina but Ferrari then revealed they had changed his car's battery, triggering an automatic penalty for a breach of the regulations.
The governing FIA confirmed in a technical report that Leclerc was now using his third energy store for the season, one more than allowed.
Ferrari are 21 points behind leaders McLaren, last champions in 1998, with 44 still to be won on Sunday and third-placed Red Bull out of the running.
McLaren principal Andrea Stella, who was previously at Ferrari, said there was no sense of the pressure being off, however.
"We talk about Charles Leclerc. We talk about Ferrari. It's a very strong combination," he said.
"I think even with the penalty, I wouldn't be surprised if we can see them very rapidly fighting for the front, for the top positions. So nothing changes."
Leclerc lapped with a best time of one minute 24.321 seconds, with McLaren's Lando Norris 0.221 slower and the Mercedes pair of seven times world champion Lewis Hamilton and George Russell third and fourth.
Hamilton was being investigated by stewards for allegedly impeding Norris, however.
Sunday's race will be Hamilton's last for Mercedes before joining Ferrari as Carlos Sainz's replacement.
Alpine's Pierre Gasly was fifth fastest, with new Australian teammate Jack Doohan only 19th in preparing for his first race as a replacement for Esteban Ocon.
Nico Hulkenberg was sixth for Haas with Williams' Franco Colapinto seventh but facing a five-place grid drop for gearbox changes. Colapinto's teammate Alex Albon will have a similar penalty.
In a Formula 1 first, two brothers took to the track for the same team in the same session - Leclerc being joined by younger brother Arthur (18th) in the other Ferrari usually driven by Spaniard Sainz.
Six of the 10 teams had a young driver at the wheel of one of their cars, fulfilling an obligation to give them track time.
Japan's Ryo Hirakawa replaced Oscar Piastri at McLaren, Isack Hadjar drove quadruple champion Max Verstappen's Red Bull, and Felipe Drugovich was in Lance Stroll's Aston Martin.
Ayumu Iwasa stood in for fellow Japanese Yuki Tsunoda at RB and Luke Browning for Alex Albon at Williams.