Caley Thistle were resilient throughout the match but were unable to make the breakthrough in an entertaining match at the Tulloch Caledonian Stadium.
Hughes was delighted with his defence, though, and singled out Gary Warren for special praise.
"I felt we had the better of the clear-cut chances. On another night we just need one of our chances to go in," Hughes said.
"We played well in the first half and passed the ball well. In the second half we dropped a little bit too deep but you are going to get games like that.
"We're playing against Aberdeen, who are a massive club compared to us. We're always punching above our weight. Every time we play them they know they've been in the game.
"I thought the two centre-backs were outstanding. Gary Warren probably just edged it. I'm delighted we kept a clean sheet and once again, Ryan Christie came on and showed he's going to be a big player for the future."
Aberdeen counterpart Derek McInnes also felt his team could have taken all three points from the match, as the visitors continued their good recent run of form against Inverness.
McIness was also happy with the way his team showed no ill effects from last weekend's Scottish Cup semi-final defeat to St Johnstone.
"That performance showed that there was no hangover from last weekend. I'm delighted with the response from the players and it's a performance I expected," McInnes said.
"Prior to this season we didn't get too many results against Inverness but we've only lost once against them this season and that was because I picked the wrong team.
"It's always a difficult game when you come up here and I thought we were terrific against the ball and they didn't play with any real fluency.
"I thought we had the better chances but with Billy McKay on the pitch you can never be comfortable. He's a predator.
"One thing that is doing my head in at the moment is our reluctance to shoot at times. We're getting into good positions and we need to chance our arm."