A centre-half whose progress ensured him a place on the bench against Chelsea in the Premiership on 10 February 2008. He was a defensive rock in Gary Ablett's reserve side who won the Premier League North title. Ablett had a high opinion of the defender: "He has an eye for a pass, good composure on the ball, he's physically stronger and can compete against the more robust forwards. He can also use his brain to deal with the smaller, quicker ones, so he's another one who is going to be a very good player." San José Domínguez appeared in several of Liverpool's pre-season matches during the summer of 2009. However, a few days before a new League season began, he was loaned back for a year to Athletic Bilbao, the Spanish club from which Liverpool had bought him two years earlier. San José Domínguez played 30 games and scored three goals in the 2009/10 season for Bilbao in La Liga and the Europa League and joined them permanently on 19 May 2010 when he signed a five-year contract, with a buyout clause of €30 million.
Dominguez was not a regular for Bilbao in the 2010/11 season but certainly had a day to forget when he played in the Basque Derby away to Real Sociedad in San Sebastian. The visitors lost two-nil with the young utility player conceding a penalty in the first half before putting through his own net in the second half. He was a part of the successful Spain squad who won the u-21 European championships in 2011 although he didn't feature in the final tournament. He only played in La Liga ten times for Bilbao in 2011/12 but he added four more appearances in the Copa del Rey and another three in the Europa League as Athletic's thrilling European run took them through to the final. Sadly, they lost both that final and the Copa del Rey final. Dominguez was an unused substitute in both finals.
Dominguez became more of a regular in 2012/13, appearing in thirty-three La Liga matches for Bilbao as well as making four appearances in the Europa League and two in the Copd del Rey. He scored six goals during the season.
The central defender played in 25 La Liga matches for Bilbao during the 2013/14 season and made a further five appearances in the Copa del Rey. Athletic finished the league season in 4th place, which meant qualification for the play-off round of the 2014/15 Champions League. Dominguez scored five goals during the season, all in league matches. In September 2014 he appeared for the Spanish national team for the first time in a friendly against France and scored the opening goal of the 2015 Spanish Super Cup when he struck from fifty yards in a 4-0 win over Barcelona. He enjoyed another sound season in 2015-16 and was called into the Spain squad for the European Championships.
In 2018-19 Dominguez completed his tenth season in Bilbao, appearing 33 times in the league and captaining the side on one occasion.