It was an end to a streak for the Claret and Blue as they were edged 2-0, effectively crashing their seven-match winning run in the league.
Ryan Sessegnon and Floyd Ayite stung the Villans at Craven Cottage.
"I think today was always going to be about who could get the first goal. Unfortunately we didn't," Bruce said.
"We had a few good chances in the first half but we weren't clinical enough.
"We were dealt a blow before the game with injuries to Jack Grealish and Albert Adomah.
"Over the last four or five weeks they've been the ones who've given us that cutting edge and penetration.
"But as I said, I always thought it was going to be a case of who scored that first one.
"They got it, and the second one is a mistake – it hasn't come off for Sam Johnstone. We got punished there."
Back to third on the league table, Villa host Preston North End in their next game on Tuesday.
And it looks as though Adomah will be out at least one more time.
"With Jack, it's a case of wait and see," said, Bruce.
"I don't think so with Albert – it's still too soon."
Adomah is Villa's top scorer in the Championship this season, having notched 13 goals thus far.