Brazil forward Rodrygo thrived in the absence of the suspended Vinicius Junior, scoring both goals in Sunday's straightforward victory.
Top scorer Jude Bellingham was back in the Madrid squad after two games out following a red card and the influential England star set up Rodrygo's second goal.
The Brazilian's opener came with a powerful shot into the top corner from just outside the area after eight minutes at the Bernabeu.
Also back in Madrid's squad was central defender Eder Militao, who had been out for eight months because of a knee injury. He came off the bench in stoppage time to loud cheers.
Fourth-placed Athletic have injury concerns over defender Yeray Alvarez, who limped off with an apparent muscle injury in the 25th minute - putting him in doubt for next weekend's Copa del Rey final against Mallorca.
Cristhian Stuani scored in stoppage time as Girona beat Real Betis 3-2 to move closer to securing a top-four finish.
The home win strengthened Girona's hold on third place.
They are nine points ahead of Athletic in fourth and 10 in front of fifth-placed Atletico Madrid, the first team outside the Champions League qualification places.
Girona twice relinquished the lead against seventh-placed Betis, but earned victory thanks to Stuani's goal from inside the area two minutes into stoppage time.
Artem Dovbyk scored the other two goals for the hosts, while Willian Jose got on the board twice for Betis, whose losing streak stretched to four games.
Relegation-threatened pair Celta Vigo and Rayo Vallecano drew 0-0, while sixth-placed Real Sociedad picked up a third straight victory with a 1-0 win at Alaves.
Jon Pacheco scored the winner with a diving header in the 59th minute.
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