Verstappen was twice penalised for forcing another driver off the track in the early laps in Mexico.
The Dutchman received a 10-second penalty for each transgression, which translated into a 24-second pit stop.
He ultimately crossed the line sixth and dropped 10 points to title rival Lando Norris.
Verstappen started the race on the front row and took the lead from Carlos Sainz at the opening corner.
He then led until shortly after the Safety Car restart for the Lap 1 crash that accounted for Yuki Tsunoda and Alex Albon.
With Sainz back through, the championship leader then came under pressure from Lando Norris.
The McLaren driver looked to pass into Turn 4 on Lap 9, but Verstappen blocked his path and ushered him off the road on corner exit – Charles Leclerc scampering through for second in the process.
Norris bounced over the grass and rejoined ahead of the race leader, quickly handing the position back to the Ferrari.
With Norris ahead of Verstappen exiting Turn 6, the Dutchman attempted a move up the inside into Turn 7, running wide and forcing both cars off the track.
The two incidents were investigated with the Red Bull Racing driver found at fault in both cases.
“I just drive how I think I have to drive,” Verstappen explained.
“Last week, that was all right; this week, 20-second penalty.
“Honestly, 20 seconds is a lot, but I’m not going to cry about it,” he added.
“I’m also not going to share my opinion.
“The biggest problem that I have is that today was a bad day in terms of race pace.
“That was quite clear again on the mediums and on the hard tyres.”
While the Turn 4 clash was potentially debatable given the positioning of Norris as the cars reached the apex, the move into Turn 7 was a slam dunk.
“I just felt that the Turn 4 was a bit more of like a question mark,” Verstappen reasoned.
“Turn 7 is what it is. That’s it.
“Honestly, those two things are also not my problem,” he added.
“The problem is that we are too slow, and that’s why I’m being put in those kinds of positions. That is my problem.
“To get back to sixth was alright, but then I couldn’t even find the Mercedes cars in front.”
Verstappen finished 59.5s behind race winner Carlos Sainz, while Lewis Hamilton in fourth was 44.8s back from the Ferrari.
Without his penalties, there was a chance Verstappen could have finished two places better than he did. That would have translated into four more world championship points.
Ironically, though he lost 10 points of his title advantage to Norris, he remains 47 clear and arguably in a stronger position now than he was heading into the Mexico City Grand Prix.
Ahead of the weekend, Norris needed to outscore his title rival by an average of 11.4 points per event.
In Mexico, he fell short of that, which pushes the average points required out to 11.75 with four races remaining.
The next of those, the Sao Paulo Grand Prix, begins on Friday.
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