As the Ghanaian midfielder rejoiced, his compatriot was left red-faced as he was sent off for a second yellow card offence.
Partey came off the bench on 72 minutes for Jose Maria Gimenez with Atletico leading 3-0 via a first-half brace from Kevin Gameiro and a Saul strike.
He rewarded coach Diego Simeone with his goal following a quick one-two with Angel Correa to shoot low into the net and send his side up 4-0 on 72 minutes before Fernando Torres came on to score the fifth.
Moments earlier, Boateng had been shown a second yellow card for raising his arm during an aerial contest that left defender Gimenez sprawling on the floor.
The 30-year-old striker was magnanimous as he helped the defender back up to his feet before exiting the pitch to the sound of applause from the home crowd.
This incident came a day after Boateng extended his stay with the club where he has enjoyed personal success since scoring 10 goals in his first season, his best ever goals haul.