Alvarez missed Atletico's three group sessions late last week because of what the club described as "an indisposition", before training alone at Majadahonda on Friday afternoon.
He was left out of the squad for Saturday's 3-1 win at Sevilla, a result that briefly shifted attention back to the pitch.
"The plan is crystal clear. Julian had a few days where he wasn't feeling well. Yesterday he trained and we hope he'll be back in action quickly and be available for the next LaLiga match. I've been speaking to him as normal," Mateu Alemany, Atletico's director of men's professional football, told reporters before the Sevilla match.
The LaLiga transfer window closes on Tuesday and the situation remains tense.
Atletico chief executive Miguel Angel Gil Marin accused Barcelona of dishonesty last week and said Alvarez would never be sold to them.
According to sources close to the situation, Arsenal are the only viable alternative should the Premier League club make an offer of around €150 million ($174 million).
Alvarez said during the World Cup that he "wanted to fulfil his dream" of playing for Barcelona.
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