Vinicius was left out of the starting lineup for arguably Madrid's biggest game of the season in Manchester as they tried to overturn a 2-1 first leg deficit.
The Brazil international reacted by skipping a prematch warm up with other substitutes, and was spotted by Zidane using his phone in the dressing room.
The coach responded by leaving Vinicius on the bench throughout the 2-1 loss, a decision which surprised observers at the time.
AS reported that the winger had phoned Zidane during the subsequent post-season summer break to apologise for his behaviour.
However sources told ESPN that in fact the apology came later, face-to-face, in the manager's office at Valdebebas.
ESPN has previously reported that Zidane's management of Vinicius has been a source of friction between the coach and senior figures at Madrid.
There are high hopes for the youngster at the club, and a feeling that Zidane does not share those expectations.
Vinicius has not featured as regularly as might have been expected this season despite the absence of Eden Hazard, his main rival for a place on the left.
The forward has started 11 league games out of a possible 23 so far in 2020-21, coming off the bench in nine more, while four of his six Champions League appearances have come as a substitute.
Vinicius has started the last three matches, however, and will be hoping to do the same in Madrid's Champions League round-of-16 first leg at Atalanta next week.
He has not scored a goal in any competition since Madrid's 3-2 defeat to Shakhtar Donetsk in October.