The former Celtic and Dundee United midfielder headed home a Jonny Hayes cross eight minutes into the second half to add to James Fowler's first-half own goal although the Dons had to hold on after Killie substitute Kris Boyd struck to set up a cagey finish to the match.
Flood admitted his side should have made sure of victory sooner, saying "If I was being bit critical we should have killed them off because we created enough chances to win two or three games today.
"On another day it'd have been a lot more comfortable. We won in the end and that's all that matters."
The Dons turned in a stylish performance in front of over 13,000 fans at Pittodrie, a hint of the interest a strong side can generate in the Granite City. However, Flood is not tempting failure by setting lofty targets.
"Our main goal is to finish in the top six because Aberdeen haven't finished in the top six in a long time," he added. "We want to express ourselves and get into the top six, and then take it from there.
"We definitely have enough quality and enough strength in depth. It's not just 11 players out there it's the whole squad and the gaffer has brought a good squad together."
The 28-year old credited assistant manager Tony Docherty with providing the inspiration what was a rare headed goal.
Flood joked "I think I last scored one when I was 12!
"Tony was on at Ryan Jack and myself at half-time, saying that he thought we could take a gamble and get into the box - I thought I'd try to shut him up and try and score a goal. I timed the run perfectly, stuck the nut on it and thankfully it went in."
Although Kilmarnock manager Allan Johnston was pleased with the way his side refused to lay down meekly and fought their way back into the game, he admitted his side still needs strengthening before the transfer window closes at the start of September.
"We lost that many players in the summer, we knew it would require massive rebuilding," he said. "We need to bring in another four or five players, at least. I think 12 left in the summer alone. We know it's a big ask."
Asked if he felt a particular area of the team required reinforcement, Johnston admitted "Everywhere! We need to strengthen every position. We've got a really young squad, with a lot of young players."
And from starting the season with a depleted squad, the former Queen of the South boss fears one of the players he does have may be taken out of the picture by injury.
He said: "Young Rory McKenzie looks as though he's picked up a sore one today which is obviously another one less for the squad."