Verstappen's Red Bull collided with Rosberg's Mercedes on the exit of the first corner after the start in Mexico City, while trying to overtake Rosberg for second.
The Red Bull driver later overshot a corner trying to pass Rosberg again, and was penalised post-race for going off the circuit while defending third place from Sebastian Vettel's Ferrari in the closing stages.
Wolff reckons this penalty was partly the consequence of Verstappen's earlier aggression while fighting Rosberg.
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"I think maybe the penalty he got at the end was the consequence of all the driving," Wolff told reporters after the race.
"As refreshing as it is, and how ruthless the great ones are, if you race the championship leader three races to the end, wheel banging is not what should happen.
"I think it's very refreshing how [Verstappen] drives, his driving is ruthless. I like that.
"I think the team gave him a radio call, and said 'keep it clean with Nico'.
"This is exactly what I would have said to him - you don't bang wheels with the championship leader three races from the end.
"The team is giving him that guidance, but maybe in the car when the visor is down it's difficult."
Rosberg finished second in Mexico, to maintain a 19-point championship lead over Mercedes team-mate Lewis Hamilton with two races remaining.
He thought his race was over after the hit from Verstappen at Turn 1.
"He went over the limit, locked up the front tyre, ran wide, and shoved me off the track," Rosberg said.
"It was a pretty big impact. It doesn't look that big on TV, but feeling-wise it was a massive impact.
"I thought, 'OK, my car is done'. My steering actually had a bit of an offset after that.
"But penalty or not that's not for me to judge. They decided no penalty. I accept that."
Red Bull boss Christian Horner defended his driver's aggressive moves on Rosberg.
"He sees a gap and he goes for it, which is what makes him such an exciting driver," Horner said.
"Nico's championship isn't Max's responsibility."
Verstappen's team-mate Daniel Ricciardo suggested Hamilton should have been penalised for locking up at Turn 1, going off the track, and gaining an advantage, but Wolff felt the decision not to penalise Hamilton or Verstappen for their first lap incidents was ultimately correct.
"It was lap one, to our defence, so that's different, [and] it wasn't in defending a position," said Wolff of Hamilton's moment.
"I think that's why the stewards were liberal in that first corner, because they didn't penalise Max either.
"Weighing up the two, it was probably the right call for both."
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