The Bristol City boss was hoping his keeper David James could celebrate a victory on his 900th career appearance but he was left instead halpless as two o.g.'s lost the game for the home side.
McInnes said: "David is an outstanding professional and hardly ever misses training, let alone a game.
"We so wanted to mark his 900th game with a win. The lads gave everything and to be beaten by two deflected efforts is hard to take.
"I'm disappointed by the result but not the performance. If the players continue to give that amount of effort we will get the points we need to be safe.
"We made positive substitutions to try and win the game, but would have been happy with a point. Now we have to show the same determination on the road."
Cardiff went in front in first-half injury time when Mason's driven cross from the right took a glancing deflection off central defender McManus.
And it was a similar story three minutes from time when another Mason cross-shot hit Cisse to wrong-foot James.
The hosts had levelled seven minutes into the second half when Richard Foster broke down the right and pulled the ball back for Jon Stead to sweep it home via the near post.
Brett Pitman hit the outside of a Cardiff post and forced a fine save from David Marshall in an action-packed finale.
Cardiff boss Malky Mackay said: "I thought we shaded the game against a side fighting for their lives. We looked the more likely winners in the second half.
"I haven't spoken to Joe Mason about the goals, but if I were him I would claim both. He gets into some great positions and today our midfielders found him with some quality passes.
"I was delighted with the way we played. I thought we did well at Brighton in midweek only to concede late on and we carried on in the same fashion today.
"Derek McInnes is a good friend of mine and I knew his team would reflect his character so we expected a tough game."