The Red Bull driver's charge from 11th to fifth was hampered by the full safety car after Logan Sargeant's crash, handing a cheap pitstop to the medium tyre starters.
His alternative strategy to start on the hards meant he couldn't take advantage of it with too long left in the race to make a switch to mediums last.
Verstappen also felt the virtual safety car that came later when Esteban Ocon stopped on the track wasn't beneficial either, as he didn't have another set of fresh mediums like the Mercedes pair.
Despite this, Verstappen's tyre advantage on the medium compound over the closing laps allowed him to carve up the order to an eventual fifth after George Russell's last-lap wall smack put him out.
The reigning F1 world champion felt without either of these safety cars he could've climbed higher, having finished just 0.264s behind Charles Leclerc at the chequered flag and 21.4s off winner Carlos Sainz.
"Everything went against us as well in the race with the safety cars, so it was possibly the worst-case scenario, as I really think if the safety cars worked out a little bit more in our favour I would've been fighting with the guys [at the front]," Verstappen said.
"Especially with the last stint that was quite easy."
He added: "It is not what we wanted but I think today was better, a little bit better, but we were still unlucky during the race with all the safety cars going against us.
"Clearly we learned quite a bit from today and maybe what we did wrong yesterday, I can't go into details, but the problem is we can only show it next year if we come back if it is better or not."
Perez, who also suffered in Red Bull's nightmare qualifying and started 13th, rose to eighth place at the finish but endured on-track incidents with Yuki Tsunoda at the start and Alex Albon later on. His clash with Albon earned him a post-race five-second penalty but didn't cost him a position in the final results.
"It's better than nothing," Perez said, having picked up front wing damage at the start. "To get out of here with a few points is not bad. But it was a complete disaster of a weekend."
Red Bull's difficult Singapore GP marked the end of both Verstappen's consecutive wins streak and Red Bull's 100% victory record in 2023.
The Dutch driver felt it showed Red Bull still needs to be "perfect" in order to maintain its dominance over the F1 field.
"Everything needs to be perfect. Everyone is always saying, 'ah look how dominant they are and look how easy it is', but it is never easy," he explained.
"A lot of details that we need to get right and this weekend clearly we didn't get a few things right and then you are on the back foot."
