The Argentine World Player of the Year initially appeared to have suffered a more serious injury after colliding with Benfica goalkeeper Artur late in the 0-0 draw at the Nou Camp but tests ruled out anything worse than bruising.
"The Barca number 10 trained with the rest of his team mates on Saturday and (coach) Tito Vilanova has decided to take him to Seville," the club said in a statement on their website.
"The Argentine footballer has recovered from the bruising to the bone on the outside of his left knee which meant he had to be taken off the pitch on Wednesday on a stretcher," they added.
"After the collision with Benfica keeper Artur the Barca forward had been working hard to be available for the coach as soon as possible."
Vilanova suggested Messi would be included in the starting 11, as his unbeaten side seek a 14th win in 15 matches this season.
They top the table with a La Liga record 40 points, six ahead of second-placed Atletico Madrid and 11 ahead of arch rivals Real Madrid in third.
"If there was any risk of injury Messi would not be travelling," Vilanova told a news conference at Barca's training ground.
"Today he trained well without any discomfort," he added. "There are still a lot of hours before the game."
Messi has the 40-year-old record for the most goals scored in a calendar year firmly in his sights.
The 25-year-old, favourite to secure a fourth straight World Player award when the winner is announced next month, has 84 for club and country in 2012, one short of Gerd Mueller's tally of 85 set for Bayern Munich and Germany in 1972.
Barca also have Alexis Sanchez, Dani Alves and Marc Bartra available for the Betis game after the trio were declared fit by club medical staff on Saturday.
The club have struggled playing away against Betis in recent times and have only managed one win in 11 matches at the Benito Villamarin stadium since 1999.