During lap 2, anticipating a call about the auto, the team told the Race Director they were calling the vehicle into the pits at the end of lap 2.
However, as the trio behind them headed into turn one, Leclerc had managed to fend off Hamilton on his inside but had Verstappen driving alongside him on his outside.
Verstappen had enjoyed a strong start to Sunday's race, and, having started from fifth, was challenging for second, when Leclerc wiped him out.
The stewards initially ruled that the contact was a racing incident, before deciding the review the collision after the race - something else that sparked the ire of Verstappen.
The Ferrari driver was forced to pit due to damage to his front wing, but recovered to finish sixth, though post-race penalties for him and his team led to that becoming seventh. "Normally you need to anticipate those things and I didn't".
And after the chequered flag, it was deemed Leclerc should be penalised 15-seconds for his actions.
Ferrari's Leclerc was dealt a double time penalty following the coming together with Verstappen, who had to retire after 14 laps following the damage inflicted on his Red Bull.
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Leclerc was handed a five-second time penalty for the collision after the race, but a different incident involving the other Ferrari driver also left Verstappen annoyed.
The resultant time penalty of 15-seconds has dropped Leclerc from sixth to seventh position at the 2019 Japanese Grand Prix. He bashed Leclerc, saying he was for hard racing, but what happened was irresponsible. "This was just irresponsible driving into Turn Two".
"We had a really good start for once, so that was the positive and then I just stayed on the outside", Verstappen explained.
In a statement, Formula One's governing body, the FIA, said: "By not bringing Leclerc into the pits at the end of lap one when there was damage clearly visible, and then by telling the driver to remain out for an additional lap, the team created an unsafe condition which only narrowly avoided being a major incident".
"Obviously I understeered being behind Seb and Lewis, and then we touched", said Leclerc. I felt like I was in third, but then suddenly into Turn 2, Charles just drove into the side of my auto. "Overall I don't think it was costing too much". We all know that you lose downforce behind the vehicle so that is not an excuse and I think he is experienced enough to know that.
"I don't know what happened in the full situation from outside and this is what I need to look at, but from the auto, it was just a tricky situation". All of them. There was only a hole in the side of the auto. I enjoy tough racing but I do not believe that was challenging racing.