The 71st minute substitution was the second appearance for the 23-year-old Ghanaian midfielder in this season’s competition.
The visitors took the lead with a well struck left-footed shot by Saul into the back post on 17 minutes as they started the game with a lot of confidence which brought early opportunities.
They doubled their lead on 25 minutes when Antoine Griezmann found himself freed by Kevin Gameiro who kept two defenders busy, and the French striker coolly slotted home.
The hosts got one back through Karim Bellarabi three minutes after the break but Gameiro restored the two goal cushion soon after when he won and converted a penalty in a terrific man of the match performance.
Coach Diego Simeone sent on Partey in place of Gameiro to shore up the midfield and keep their advantage soon after they conceded an own goal after goalkeeper Angel Moya tipped a save onto the knee of Stefan Savic.
Substitute Fernando Torres then scored a header four minutes from time to ensure they took a two goal cushion to Madrid for the return leg in a fortnight.