With rain falling steadily right at the start of Q3, all the drivers knew that their best opportunity to put in a time would come right at the beginning of the session.
Magnussen, who led the cars out of the pits, had the best of the conditions and pulled off a brilliant lap to grab a shock maiden pole position for both himself and his Haas team.
But Verstappen, who had been favourite to take the top spot, reckons he would have ended the session on top if he did not make a mistake halfway around the lap.
The world champion said that a small lock up at Turn 8 – the tight right-hander after Laranjinha – made the difference as deteriorating conditions meant there was no second chance to improve, especially after the red flag stoppage for George Russell's off.
“We knew that it was going be that one lap, because there was the potential rain,” explained the Red Bull driver.
“I think I was like the fourth or fifth car, and I locked up into Turn 8. So that's, of course, cost me pole today.
“But still, compared to the proper opposition for tomorrow, it's looking good. And, in these conditions, anything can happen. And we are still up front, which is the most important.”
Verstappen admitted that the changing conditions through qualifying, which started damp in Q1 then dried out before it rained again for Q3, had made it especially tricky to judge how much risk to take.
“It was difficult,” he said. “You have to find the limit of how much you can push. But then also, you don't want to have big mistakes and potentially drop out.
“So we just stayed calm from Q1 to Q2. Then Q3 was a little bit more of a lottery. But nevertheless, I’m still on the front row.”
Verstappen starts one place in front of Mercedes driver Russell, with Ferrari’s Charles Leclerc left languishing in 10th after Ferrari sent him out on intermediates at the start of Q3.
And with Saturday’s sprint race giving Verstappen a chance to move forward before Sunday’s main grand prix, he was relaxed about the situation.
Asked if, with the championship now done, he could take more risks and have fun in the sprint, Verstappen said: “I will always try to have fun, but I think the approach should always be the same.
“But yeah, let's see how competitive we're going to be tomorrow in the race. Also the weather. I have no clue what's going to happen. But that is what makes Interlagos always very special for everyone.”
