Atletico Madrid were set to finish as the runners-up in Spain's top flight until they conceded a last-gasp leveller against Villarreal, leaving them in third, one point behind second-placed Los Blancos.
Athletic have also missed out on the chance to claim European football for next season, ultimately finishing eighth in the division, two points behind seventh-placed Osasuna, who will be present in the Europa Conference League playoff round.
On Sunday morning, it was announced that Benzema would be leaving Real Madrid this summer, with the Frenchman widely expected to make a big-money move to Saudi Arabia.
Benzema signed off in the best possible way, scoring a leveller from the penalty spot in the 72nd minute, while there was also a final appearance for the club for Marco Asensio, who is departing on a free transfer, with the Spaniard set to join Paris Saint-Germain.
Athletic were awarded a penalty in the ninth minute of the match when the ball struck Toni Kroos's arm inside the box, but Mikel Vesga saw his spot kick saved by Thibaut Courtois.
Vinicius Junior - back in the side after injury - and Rodrygo both brought smart saves from Athletic goalkeeper Unai Simon in the first period, but the visitors were the more dangerous side in the opening 45, with Courtois also denying Yuri Berchiche and Gorka Guruzeta during a positive first period for the Basque side.
Athletic deservedly took the lead in the 49th minute, with Oihan Sancet finding the back of the net at the second time of asking after seeing his initial shot saved by the Real Madrid goalkeeper.
Asensio was introduced in the 58th minute of the match, replacing Dani Ceballos, who also only has a contract with the capital giants until the end of the month.
Ancelotti hinted ahead of the match that both Ceballos and Nacho had been offered new deals, with the pair now deciding whether to sign on the dotted line or seek pastures new.
Real Madrid were awarded a penalty in the 71st minute of the match when Yuri challenged Eder Militao, and Benzema stepped forward to score, firing his spot kick straight down the middle.
The Frenchman left to a standing ovation in the 74th minute, and an announcement on his future is set to arrive next week, with Al-Ittihad expected to sign him.
Luka Modric and Kroos were also involved on Sunday, and the pair will see their contacts expire at the end of June, but both are widely expected to sign extensions until next summer.
Eden Hazard and Mariano Diaz, who are both leaving this summer, were ultimately unused substitutes against Athletic, with Ancelotti deciding against giving them late cameos.
Real Madrid have ended the season with the UEFA Super Cup, Club World Cup and Copa del Rey trophies, as they fell short in both La Liga and the Champions League.