Rafinha, the younger brother of Bayern Munich and Spain midfielder Thiago Alcantara, has been sidelined with a muscle injury while Vermaelen, who joined from Arsenal in the close season, has been suffering with a hamstring strain.
"He (Rafinha) is feeling good and the discomfort has disappeared," Luis Enrique said at a news conference previewing the game in Madrid.
"After virtually not playing last season, we won't take any risks (with Vermaelen)," he added. "He will be back with us and at full fitness soon."
Barca are looking to bounce back from Tuesday's 3-2 Champions League reverse at Paris St Germain, when the Ligue 1 title holders exposed weakness in the La Liga side's defence similar to that which dogged them last season.
Going into the game at the Parc des Princes, Barca had not conceded a goal in seven outings in all competitions and they are two points clear of Atletico Madrid and Valencia at the top of La Liga after six matches.
Rayo, who have started the season brightly and are ninth in the standings, have won praise under coach Paco Jemez for a playing style that like Barca's relies on keeping the ball and pressing their opponents high up the pitch.
"Rayo is a team I especially like," Luis Enrique said.
"They are an example of an attractive side without much of a budget," added the former Barca and Spain midfielder, who is in his first season in charge at the Nou Camp.
"Both teams (Barca and Rayo) want the same thing. We believe that having the ball is fundamental to victory. The idea of taking control of the game is clear for both."
Saturday's game is another chance for Barca's Lionel Messi to draw closer to the La Liga scoring record of 251 held by Telmo Zarra.
Argentina captain Messi, who has netted five times in La Liga this term, has 248 overall.
(Reporting by Iain Rogers, editing by Ian Chadband)
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