Elsewhere Real Valladolid were relegated after a 0-0 draw with Getafe, while five other sides near the bottom were able to breathe a sigh of relief after a gripping conclusion to the season.
Champions Barcelona were beaten 2-1 at Celta Vigo, with Gabri Veiga's brace ensuring the Galician side will remain in the top flight next season.
Benzema, whom Madrid confirmed would leave this summer earlier in the day, departing after 14 years at the club, rolled his penalty down the middle to level the game, before being substituted to great applause.
The draw ensured Real Madrid would finish above city rivals Atletico Madrid in second place after Diego Simeone's side tied 2-2 at Villarreal on the final day.
"I spoke with him this morning and he told me he was going. He's taken the decision and I told him I respect it completely," said Real Madrid coach Carlo Ancelotti.
Ancelotti said Benzema's choice came by surprise after the Italian himself said on Saturday he expected the forward to stay.
"I have coached one of the best in the world, not a forward, a complete footballer," continued the coach.
"A very friendly, humble, serious person. We can't be happy he is going, but we have to respect his decision. What he has done at this club is legendary and unforgettable."