Real Madrid won 2-0 at Athletic Bilbao on Sunday and the duo appeared from the bench, with Eduardo Camavinga (20) and Dani Ceballos (26) starting ahead of them.
Modric and Kroos - both out of contract at the end of the season - face stiff internal competition this season, with Ancelotti highlighting that Madrid are in a period of transition.
"They are professionals and understand what this club means," Ancelotti told reporters ahead of Thursday's Copa del Rey quarter-final with Atletico Madrid.
"They know the quality this squad has and I don't think I have to explain anything.
"We've been speaking from the start of the season about this topic, it's a moment of transition and everyone has to understand it, the young players and the veterans."
Modric joined Real Madrid in 2012 while Kroos arrived in 2014 and together they have formed an essential part of the team's success.
They have won three La Liga titles and four Champions Leagues together, among other silverware.
Until this season they had Casemiro (30) behind them too, but the Brazilian moved to Manchester United last summer, with Aurelien Tchouameni (22) taking that role this season.
Ancelotti said despite being dropped against Athletic, the duo will still play an essential role for Madrid.
"Of course they can play together, they are performing this season and have been key, and they will keep on being so," added the coach.
Ancelotti admitted that Fede Valverde (24), another midfield option, has not hit his best form again after the World Cup.
The Uruguayan was spectacular in the first half of the campaign but is struggling to return to those heights.
"He's not at his best level, he's progressing, he's performing - not like in the first half of the season, I consider that normal given the World Cup," said Ancelotti.
"We have to be patient. We're not asking him to score goals, we're asking him to deliver defensively and in attack, and when he's back to his best he will score again."
EYEING SILVERWARE
Ancelotti maintained unity was key for Real to win silverware this season but said that it would not be easy to overcome a resurgent Atletico.
"We are facing a special opponent in a special match on Thursday. It is an important opportunity and we want to win a title," the coach said.
"Atletico are a great rival and winning against them is always difficult. What I can say is that it's not just another game... no, it's special and it will be entertaining."
Atletico coach Diego Simeone returned the compliments but said that his team will be stronger in attack than they were before the World Cup break, with all players fit except for injured midfielder Marcos Llorente (27).
"I see the team is better since we returned from the World Cup, with much more offensive options to create danger and working very well as a group," Simeone said.
"I see the group committed, with enthusiasm and we are going to play an important game, a match with a very strong team, with a coach that I greatly admire, with everything that Real Madrid represents on the field and in their game."
In the other quarter-finals, Barcelona host Real Sociedad and Sevilla play Osasuna on Wednesday while Valencia and Athletic Bilbao face each other on Thursday.
