Sainz was timed under lights at 1min 32.120sec, 0.018sec ahead of Leclerc, as Ferrari dominated in conditions expected to be most similar to those for qualifying on Saturday and for Sunday's night race.
The Red Bulls have been unstoppable so far in 2023, winning all 14 grands prix, with flying Dutchman Verstappen taking the chequered flag 12 times, including the last 10 races in a row. Sergio Perez has won the other two.
But Verstappen, who is seeking a maiden victory in Singapore, could only finish in eighth place 0.732sec adrift of Sainz with Perez just 0.040sec quicker in seventh.
"It's just not happening, mate," Perez complained to his engineer on team radio. "Every braking zone I feel like I'm going to crash. The rear is stepping out massively."
George Russell was third in the Mercedes, 0.235sec behind Sainz, despite a scary moment when the Englishman's rear end stepped out after running wide on the final bend of a hot lap.
Fernando Alonso was fourth in the Aston Martin ahead of Lewis Hamilton's Mercedes with Lando Norris sixth fastest in his McLaren.
Singapore had been tipped to represent the biggest challenge to Red Bull's unprecedented quest to sweep all 22 races this season.
'There's a lizard!'
Marina Bay's bumpy, high downforce layout and the ever-present threat of tropical rain storms always threaten to play havoc during qualifying on Saturday and Sunday night's race.
Norris benefitted from an upgrade package newly bolted to the bodywork of his McLaren to finish ahead of the Red Bulls in both sessions.
Many observers were tipping Mercedes to close the gap on Red Bull in Singapore, but the early signs point to Ferrari having the edge, on single-lap pace at least.
The lap times were more than 10 seconds quicker than a year ago after the removal of four 90-degree corners towards the end of the lap because of construction work.
In first practice, Leclerc had led Sainz for another Ferrari one-two, with Verstappen third in a session where hot laps were interrupted three times by large monitor lizards crossing the city-centre track.
Yuki Tsunoda was one of the drivers taken completely by surprise as yellow warning flags were waved.
"Oh there's a lizard! Oh my god!" exclaimed the Japanese AlphaTauri driver on team radio.
Apart from the reptilian invasion, both sessions were remarkably incident-free with red flags absent.
There was a minor scare for Lance Stroll as he drifted wide in his Aston Martin at turn 15 and clipped a wall in second practice, but the Canadian driver escaped unscathed.
The only casualty in either session was Thailand's Alex Albon, who managed only five laps in his Williams before being forced to retire after reporting a loss of power.