The fiery Argentine said the 3-0 win over the French side in Lyon, achieved thanks to Antoine Griezmann's brace and a late Gabi goal, meant "much more than just winning a trophy".
Simeone took over a club that had been in a near constant state of disarray for more than a decade and almost immediately revived their fortunes.
But after one Europa League, one Copa del Rey and a La Liga title in his first two and a half years at the helm, the last few seasons had been defined more by the near misses.
Two Champions League final defeats in agonising fashion against city rivals Real Madrid in 2014 and 2016 had many thinking Simeone might be tempted to accept an offer from one of Europe's super clubs.
Yet the 48-year-old has toughed it out through a FIFA-imposed transfer ban, a disappointing Champions League group-stage exit earlier this season and a January window when the club sold a clutch of valuable squad members.
He has led Atletico into their new stadium and to the club's third Europa League triumph in nine years, while also keeping them on course to finish above Real in La Liga.
"It has been a difficult season, but winning the Europa League is much more than just winning a trophy, it validates all our hard work, our determination," Simeone said after Wednesday's game.
"Last season we reached the semi-finals of the Champions League, and this season we started that competition badly, but we showed our manliness against Arsenal and that set us on the way to winning the cup."
Griezmann's goal in London in that semi-final against Arsenal set Atletico on the way to beating the Premier League club, and it was testament to how far they have come under Simeone that they were the favourites to win that tie.
They clearly justified their favourites tag against Marseille too, with a typical Atletico performance -- happy to soak up the pressure and wait for an opposition error, from which Griezmann put them ahead.
Falling behind against Atletico is usually fatal, and so it proved for the French side.
Simeone's team are so well-drilled that the coach's absence from the touchline was no problem -- a suspension meant he had to watch from the stands.
Sense of belonging
This may be less prestigious than the Champions League, but Simeone has now won six titles with the club, including a UEFA Super Cup and a Spanish Super Cup.
That puts him level with the tally of the legendary Luis Aragones, like Simeone a former player who went on to coach the club.
Simeone won a league and cup double as a player with Atletico before eventually returning to his homeland to cut his teeth in coaching, but it is in the Spanish capital that he clearly feels he belongs.
"Atletico Madrid for me is an important place in my life, not just in sporting terms," he said.
"I grew as a player at this club. I came back at an important moment in my life, and without doubt returning gave me a sense of balance and peace.
"This is not just about winning the Europa League, no, it's much greater than that. It's about hard work, effort, making ourselves competitive, winning again and again."
That relentlessness means Simeone will not take his eye off the ball before this weekend's final La Liga game against Eibar, when a draw will secure second spot and allow Atletico "to continue being a nuisance" to their more powerful rivals.
Then it will be on to next season, sorting out Griezmann's future, and targeting the Champions League final, which will be played in their own Wanda Metropolitano stadium.