A 36th minute substitute in the fixture at Wanda Metropolitano, the utility man's outing saw him reach the 100th game mark for Los Rojiblancos in all competitions.
He replaced injured right-back Juanfran in the match that was decided by Antoine Griezmann's solitary strike.
"Thomas Partey has joined the 100 club," a publication on the club's official website reads.
"Our academy youth product defended our shirt for the 100th time in our match against Rayo Vallecano at the Wanda Metropolitano. These stats are presented and brought to you by bwin.
"Thomas joined our academy back in 2011 and has since then progressed through the ranks until he reached our first team in 2015.
"His debut for the first team came on 28 November, 2015 against RCD Espanyol.
"A plaque commemorating Thomas' 100 matches will be placed in the Wanda Metropolitano’s Walk of Legends.
"Breakdown of Thomas’ 100 matches for Atletico:
UEFA Europa League: 8
UEFA Champions league: 17
Copa del Rey: 10
UEFA Super Cup: 1
After progressing through Atletico's youth set-up, limited first team opportunities saw Partey sent out on successive loans to Real Mallorca and Almeria in 2013-14 and 2014-15 respectively.
Last term - his third straight season with Los Rojiblancos' senior side - the midfielder made 33 league appearances involving 28 starts and scored three goals to help the club finish second in La Liga.
He has played in all two league games so far this campaign.