Substitute Rodrygo equalised in the 79th with a delightful goal, dribbling past three defenders before finishing well.
Benzema was in red-hot form, scoring 15 times in the competition and lifting the trophy for a fifth time in his career after the Spanish side beat Liverpool in the final.
Seven times reigning winner Lionel Messi was not nominated for this year's Ballon d'Or for the first time since 2005.
Europa League winners Eintracht had offered some resistance in the first half and had chances to score but were eventually overrun by the Spaniards.
After Liverpool booked their place in the final on Tuesday, the Egyptian winger stated that he wants to face Real Madrid in the final of the competition.
Real will take on Liverpool in a rematch of the 2018 Champions League final at the Stade de France on May 28.
The hosts, who were also missing four player due to COVID-19,dominated most of the second half but Real held on to secure all three points.
Ancelotti has backed forward Karim Benzema to win the Ballon D'Or, comparing the Frenchman to a wine that gets better with age.
Ancelotti said he will demand more goals from Real Madrid’s strikers next season and promised to play thrilling, attacking football.
Messi's brace took him to the 25-goal mark, which he hit for the 12th season in a row.
The Spanish side will face Chelsea in the last four as they search for their fifth Champions League title in eight years.
Benzema missed training on Friday morning and Zidane said he will not travel with the team for Saturday's La Liga game away at Real Valladolid.
Real Madrid coach Zinedine Zidane said on Friday that there is no problem between forwards Karim Benzema and Vinicius Junior.
"Benzema is in great form, I'm not surprised. Everyone knows his quality." Varane said.
Real Madrid’s Karim Benzema produced an audacious back-heeled assist for Casemiro to score as they beat Espanyol 1-0 away on Sunday to capitalise on Barcelona’s slip-up a day earlier and move two points clear at the top of La Liga.
Real Madrid took control of the Spanish title race by beating Real Sociedad 2-1 away on Sunday to move top of La Liga above Barcelona after a second-half high on controversy.
The French striker joined Real Madrid from Olympique Lyonnais in 2009 and since then he established himself as the team's starting striker.
Real Madrid's Karim Benzema has mocked France striker Olivier Giroud by likening himself to a Formula One car and Giroud a go-kart.
Real Madrid's top scorer Karim Benzema praised his team's 2-2 draw at Paris St Germain on Tuesday in the Champions League.
Karim Benzema made it 30 goals for the season on Sunday as he led the way again for struggling Real Madrid with a hat-trick that shot his side to a 3-0 win over Athletic Bilbao.