The Bernabeu was home to a tight contest in the first half, as Spain and Sweden played out a scoreless draw in the first 45 despite La Roja having an edge in the proceedings.
But the deadlock was broken on 64 minutes, as Sebastian Larsson was called for handball, allowing Ramos to step up and put Spain ahead.
Another opportunity came 20 minutes later as Morata, a second-half substitute, was hauled down in the area late in the contest.
But rather than Ramos step up again to put away the victory, the Spain captain insisted Morata take the spot kick, which he made.
Mikel Oyarzabal completed the scoring from open play a couple of minutes after Morata’s goal to give Spain a convincing 3-0 win and leave them a perfect four wins from four games in Euro 2020 qualification.
And Morata praised Ramos after the match, telling reporters being allowed to take the spot-kick was an unexpected gesture.
"I did not even ask him [about the penalty] because Sergio always wants to put all the possible goals,” Morata said. “But he has made an incredible gesture. I thank him and he knows what I think of him."
The striker scores six times and assisted on a pair of goals in 15 La Liga games for the club, which have the option to purchase Morata on a permanent basis.
Morata has been previously vocal about wanting his future to be at Atletico, and hopes that remaining in the Spanish capital can lead him toward gaining a more prominent role in the Spain set up.
"It's time to take a step forward in Atleti and in the national team,” Morata said. “It's time to be somewhere, stable, not worrying about my future and with ambitions to win.
“I want to stay at Atlético as long as possible."