The forward came on in the 75th minute for the Group F winners, who were beaten by goals from Khvicha Kvaratskhelia and Georges Mikautadze in Gelsenkirchen.
Elsewhere in the section, Vitezslav Jaros was an unused substitute in Czechia's 2-1 loss to Turkiye that confirmed their elimination.
Results also meant Dominik Szoboszlai's Hungary did not qualify for the knockouts as a best third-placed team.
Jota will be one of seven Liverpool players involved in the last 16, alongside Trent Alexander-Arnold, Joe Gomez, Virgil van Dijk, Cody Gakpo, Ryan Gravenberch and Ibrahima Konate.
Saturday June 29
Sunday June 30
Monday July 1
Tuesday July 2
