Werner made his Primera División debut on 3 October 2015, starting in a 1–1 away draw against Arsenal.[3] In March 2016 he was chosen as a first-choice, as starter Germán Montoya was injured;[4] the latter subsequently moved to Belgrano.
On 8 March 2018, after Moyà was released, Werner made his competitive debut for Atlético by starting in a 3–0 UEFA Europa League home defeat of FC Lokomotiv Moscow. On 29 April of the following year, he made his La Liga debut by playing the full 90 minutes in a 1–0 win at Deportivo Alavés.
On 21 June 2019, Werner once again went on loan, this time to Atlético San Luis in Mexico.[8] After spending his first season as a backup to Carlos Felipe Rodríguez, he became the first-choice option in 2020–21 season, after his loan was extended for a further year.
Elche
On 1 September 2021, free agent Werner returned to Spain and its top tier, after signing a two-year contract with Elche CF.[9] After being a third-choice behind Édgar Badía and Kiko Casilla, he was loaned to Arsenal de Sarandí back in his home country the following 31 January.[10]
On 30 January 2022, Werner was loaned out to Argentine club Arsenal de Sarandí until the end of 2022.[11] On 15 August 2023, after spending the entire 2022–23 as a backup to Badía as the club suffered relegation, he moved to Rosario Central on a one-year loan, with a buyout clause.[12]