Cristiano Ronaldo's 42nd goal of the season prevented Real Madrid from suffering a second successive defeat at the Bernabeu.
Inaki Williams had put Athletic Bilbao ahead with a fine clipped finish.
But Ronaldo, who had earlier hit the crossbar with a header, diverted Luka Modric's shot in with his heel to score his 26th goal in 16 games.
Madrid stay third in La Liga, 15 points behind leaders Barcelona and three points adrift of Atletico in second.
Despite dominating for long periods, it had looked like being a frustrating evening for Zinedine Zidane's team, who squeezed through in the Champions League a week ago despite being beaten at home by Juventus.
Madrid won that quarter-final tie 4-3 on aggregate with a last-minute penalty from Ronaldo.
And the hosts, who had 29 shots on goal, appeared as though they were going to be punished for their profligate finishing, until the Portuguese forward came to their rescue again three minutes from time.
Latest Stories
-
Takoradi traders lament over low sales ahead of Easter
58 mins -
Michael Ampadu: One Student, One Tablet initiative will shape the future of education and innovation
1 hour -
I will partner you for development – Alan tells TUC
1 hour -
Malnutrition, anemia remain concern to UNICEF
1 hour -
Kasoa shrinking penis: Court remands Electrician over false alarm
2 hours -
‘I look forward to working closely with President-elect Faye to enhance Ghanaian-Senegalese relations’ – Akufo-Addo
3 hours -
Girl, 8, only survivor as 45 killed in bus crash in South Africa
3 hours -
Biden to host star-studded NYC fundraiser with Obama and Clinton
3 hours -
GDNR, AAU and others launch Universal Acceptance for local languages in internet domain names
4 hours -
Ogum and Kotoko’s March malaise
5 hours -
BushGang Zee releases new afro dancehall anthem “Accra Stay By Plan”
6 hours -
2 repair vessels dispatched for undersea cable repairs – says NCA’s latest update
6 hours -
Multimedia Group Limited’s Clinton Yeboah shortlisted for 2 International Sports Press Association Awards
6 hours -
Supreme Court upholds High Court verdict on fraudulent sale of property by Senior Police Officer
6 hours -
NHIS Biometric Membership Authentication System limited rollout satisfactory – NHIA Deputy CEO
7 hours