The Spaniard was dropped for the Champions League clash against Manchester City following the defeat to Sevilla back in September, while Ramos also responded with a gesture of "support" to team-mate Mesut Ozil after the German was substituted during the Deportivo match.
It has led to reports of falling out and arguments between the skipper and the Portuguese coach but Ramos insists all that is behind them now.
“We've had our differences at times,” Ramos told Marca.
“We have had to explain what we have always done face to face to each other, and have not heard anything from anyone [else]. My relationship with him is very good today."
The Spain international, who has 98 caps to his name, also spoke of the “honour” of possibly reaching 100 for the national side.
“For me it is an honour to have reached such a tremendous record with Spain. Also because it is very close to my 27th birthday, it is March 30 and we have two or three games before it.”
Spain travel to Panama for a friendly on Wednesday.