Although the Dons fell 5-2 to champions Celtic on Saturday, Dundee United's failure to beat Inverness meant they are bound to end the season in the top three of the Scottish Premiership.
Their lead over third-placed Motherwell was cut to a point but the League Cup winners are guaranteed to be back on the European stage for the first time in five seasons.
"It's brilliant," McInnes said. "If you said at the start of the campaign we would have a cup in the bag and be back in Europe, we would all have been grabbing that.
"The players should be really pleased with their efforts and it's testament to how hard they have worked this season. So that's another box ticked and we've got two games now to grab second spot."
Although Celtic eventually ran away with things on home soil, McInnes was pleased with his side's performance and felt the game turned on a penalty that was not given to them.
Jonny Hayes went down under an Efe Ambrose challenge but referee Iain Brines turned down their fevered appeals for a spot-kick with Celtic 3-2 in front.
"The pivotal moment in the game is without question at 3-2," he said. "It's a penalty kick. It's not only a penalty kick, it's last man for Ambrose and down to 10 men.
"I think Ambrose is a bit lazy with his defending, he gets square to the ball and sticks his leg out. He took a chance and for me it's a penalty kick.
"Ultimately Celtic scored some good goals and had some good performances and have the quality to pick you off but I thought at 3-2 the momentum was with us.
"Effectively it could be 3-3 playing against 10 men and it's game on. But we never, Celtic got the fourth goal, and we were a wee bit open at that stage because you are as well going forward and having a go."