Dembele has been out of action since he suffered a torn hamstring after coming off the bench against Lyon in the last round.
Valverde accepted he took a risk in playing Dembele in that game, the winger having been a pre-match injury doubt.
Dembele was expected to miss both legs of the quarter-final against United but returned to training earlier than expected.
"He's definitely not available for tomorrow and we'll see about Wednesday," Valverde told a news conference. "It's not worth us taking the risk with the remaining games.
"I can say tomorrow he will not be able to play. Yesterday he trained for a little while with the group, we'll see if he does today, but he will be brought back into the group gradually."
Malcom is a contender to start against Atletico having recorded a goal and an assist in Barca's last game, a 4-4 draw at Villarreal.
"He has the same chance [to play] as everyone else, we'll see tomorrow," Valverde said of the Brazilian.
"He looks good in recent games and could have had better decision-making in attacks the other day but his excellent ability is evident.
"He scored the other day and provided an assist too and he has a lot of room to grow more."
Victory over Atletico would move Barca 11 points clear of Diego Simeone's side at the top of the table, but Valverde feels the title race remains alive.
"I don't think we'll have anything special planned and neither will they, but the value of three points is important for both sides," Valverde added. "For them it's the opportunity to get closer to us and make the table a little tighter. But anything is possible in this game.
"Mathematically it isn't definitive if we win the game tomorrow. Four days ago, before Villarreal people said it was over in January with half the season left, but if you don't win they say you've lost the league. Nobody here is saying, 'The league is over until mathematically it is'.
"We have to be prepared for everything. It's possible they might have a lot of high pressure and it's true high pressing is hard to maintain, sometimes they hold back and wait. But they are organised and they like to play behind the defenders.
"Sometimes they trick you and can go on to the counter well. They need space but have great shooters like Koke and Saul [Niguez]. We'll see examples of both their styles of play throughout the game."