"We have moved on from Spa in 2014 and it was a completely different situation in the team back then," the Austrian told reporters, referring to a collision between the two at the Belgian Grand Prix.
"By continuing to let them race (each other) it was clear that eventually this could happen. And we will continue to let them race."
The second lap collision in 2014 led to a freeze in relations between the drivers, who had been friends and rivals since their teenage years.
In that incident, Rosberg finished second behind Red Bull's Daniel Ricciardo while Hamilton ultimately retired with collision damage.
The Briton said later that the German, who was blamed by the team, had declared he had done it on purpose.
Collision ends Rosberg’s run
Sunday's incident put both out of the race, with the two drivers lining up on the front row of the grid and crashing into each other as they fought for the lead through the third corner of the opening lap.
The collision ended Rosberg's run of seven wins in succession including the first four of the year and the team's hopes of a one-two finish. Wolff said the collision, which the stewards deemed a racing incident, was the result of a number of unfortunate coincidences. Neither driver was totally to blame.
"I think what matters more is how we come out of the incident as a team," he said. "We've had a really great spirit in the team in the last couple of races through many ups and downs.
"We never threw the toys out of the pram and I think that is another challenge for us, to demonstrate as a team that we can move on from difficult circumstances."
Hamilton suffered power unit problems in qualifying for the two races before Barcelona, starting at the back in China and from 10th place in Russia, but retained his composure.
The champion, still 43 points behind Rosberg with 16 races to go, said on Sunday that his first thoughts were for the team.
"That was the most gutting thing when I stopped, just thinking about all these guys that work so hard in this team to give me the opportunity to race today. To not deliver for them ... is a very painful experience for all of us."
Wolff said both drivers knew what was expected and he was "100 percent sure" it would not influence the way they worked as a team.