The Nerazzurri completed an unprecedented treble for Italian teams after defeating German giants Bayern 2-0 in the competition's final in Madrid on Wednesday.
In-form Argentinean striker Diego Milito scored two goals either side of the interval to give Inter the prestigious accolade.
"We weren't good enough to impose ourselves on the game today, and that's a shame," Dutch coach Van Gaal said after the game.
"Against a team like Inter, and with our attacking orientation, you have to be on peak form. We weren't today, but we're only human.
"The game was exactly as I expected. We attacked, and Inter reacted. It's obviously easier to defend than attack. But despite that, Inter deserved to win."
Van Gaal can still regard this season as a huge success after helping Bayern win the German double.
The Bavarians won the Bundesliga after beating off competition from Schalke before defeating Werder Bremen in the German Cup final.
"It's been a great season," the 58-year-old, who took over at the club in the summer of 2009, added.