Both players had entered the contest with a perfect 12-0 sets record at this year's Roland Garros and, after two hours and 46 minutes, it was the six-times champion who stood with his arms aloft after firing an ace on match point.
For Almagro, it was yet another defeat to his Spanish Davis Cup team-mate and his win-loss record now stands at 0-8.
Nadal's victory puts another Spaniard David Ferrer in the firing line in Friday's French Open semi-finals.
Ferrer made it through to his first Paris semi at the ripe old age of 30 after bouncing out British world number four Andy Murray 6-4 6-7 6-3 6-2 on a soggy day in the French capital.
Nadal called his friend Almagro "one of the best players of the world".
His generosity, however, was nowhere to be seen on the court. He teased Almagro during a close first set and then moved in for the kill, finishing off his opponent with his 10th ace of the match.
Almagro has now faced Nadal eight times and eight times he was left gasping for air.
"I played one of the best matches I can play against Rafa, but he's the number one of the world on this surface," said Almagro.
"I knew that I would give everything I have to give because I know that against Rafa you have to play your best tennis.
"I wanted to fight all the way against him. I fought against Rafa, but he played a perfect match."
It was Nadal's 50th win at Roland Garros and, having not put a foot wrong, signs are the no one, not even Federer and Novak Djokovic who will contest the other semi-final, will be able to stop the rampaging Mallorcan from lifting the Musketeers' Cup on Sunday.