"We had just played on Wednesday and we have the second leg on Tuesday and I thought this was the moment to make changes", said the Barca coach.
Smalling would have been public enemy number one with Barcelona fans had he seriously injured Messi, but the 29-year-old claims the clash was an accident.
In their debut La Liga campaign, Huesca are now bottom of the table, where they've been for much of the season.
Barca midfielder Arturo Vidal was happy to admit that his side's minds were more focused on getting beyond the Champions League quarter-finals for the first time since 2015 than on the game they were playing on Saturday.
"Then, since I hear that for Juventus the league is easy, well, the league is easy for those who don't win, but for those who win it's hard".
Juventus boss Massimiliano Allegri made nine changes to his starting line-up from the side which faced Ajax in the Champions League in midweek, with debutants Grigoris Kastanos and Paolo Gozzi among the starters.
Barca slowly regained momentum as, in the 56th minute, Wague got space down the right and cut the ball back to Dembele, but his effort was blocked.
How to Watch Live Telecast of Huesca vs Barcelona, La Liga 2018-19 Football Match?
The home side created the first decent opening in the 12th minute from a corner, which saw Ezequiel Avila glance a header over goalkeeper Marc-Andre Ter Stegen and wide.
Barcelona's Malcom went closest to a goal when he struck the upright in the 57th.
Juventus remains 20 points above second-placed Napoli, which visits last-placed Chievo Verona on Sunday.
The price was two points dropped and Atletico capitalised, beating Celta Vigo 2-0 thanks to a thundering Antoine Griezmann free-kick and a cool finish from Alvaro Morata.
Speaking to BBC Radio 5 Live on Thursday, Smalling said he had a "brief chat" with Messi after the game at Old Trafford.
Sevilla is in fourth place, the final Champions League spot.