Roma had reached an agreement with Bordeaux to sign the 21-year-old, subject to the player completing a medical and agreeing personal terms with the Italian club.
He is, however, set to continue his development in Catalunya as he prepares to enter into a five-year deal.
Roma supporters had even gathered at the airport in Italy's capital city to greet Malcom on Monday night, but he never arrived.
The Brazilian, who can play as a winger or attacking midfielder, will undergo a medical on Wednesday before being unveiled as Barcelona's third signing of the summer.More news: Tour de France stopped after pepper spray hits riders during roadside protest
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English clubs may have been put off from bidding for Malcom as he needed a United Kingdom work permit to play in the Premier League.
It would add even more intrigue to the fixture at the AT&T Stadium, given Barca will already have one eye on avenging last season's shock Champions League exit at the hands of the Serie A side.
But Malcom became their primary target after a campaign during which he scored 12 goals and laid on eight assists in all competitions.
Unsurprisingly, the Sporting Director of AS Roma, Monchi, is disappointed and confused by the news that a deal he thought was done was spoiled at the last minute by an approach from Barça.