Highlights Atletico Madrid 1-1 Eibar September 15 2018
Borja, 19, fired home from 10 yards in the last minute of injury time.
Atletico had missed a number of chances and looked to be heading for defeat after Sergi Enrich scrambled in an 87th-minute goal for the visitors.
Atletico have now only won one of their opening four La Liga matches.
The 2013-14 champions are fourth in the table, four points behind Barcelona and Real Madrid who both have a game in hand.