The Argentina international had failed to assist a goal or score from open play in six league matches before Saturday's victory.
It was the first time he had been benched for a league game since September 2019, but Koeman insists he was left out purely for fitness reasons.
"We talked yesterday," Koeman said to Movistar Plus. "Leo came out of the game against Dynamo Kiev with some discomfort and was not in a position to play from the start today.
"We had to put him on the bench. If he has no problems then he plays from the beginning. Today he could not."
Messi was brought on at half-time and scored a brace as a substitute for the fifth time in his career and the first time since May 2013 – also against Betis.
"I have no doubts about him," Koeman said. "I know him well and see him train every day."
Barca went into half-time level after their academy product Antonio Sanabria cancelled out Ousmane Dembele's strike, roughly 15 minutes after Antoine Griezmann had a penalty saved.
Messi inspired his side to a first win in five league games, however, by playing a pivotal part in Griezmann's strike and converting a penalty awarded for Aissa Mandi's handball.
Mandi was sent off but Loren Moreno scored to make things interesting, only for Messi's first open-play goal this term and Pedri's maiden LaLiga strike to settle things.
"It was an important victory for us because we needed the points," Koeman said. "I'm happy because we created a lot of chances, had opportunities to score and did score.
"Luckily, we scored in the second half because the first half wasn't fair. Conceding a goal against a team with 10 men also isn't good, but it was a deserved victory."
Griezmann missed three big chances in the first half, as well as a penalty, which ex-Barca stopper Claudio Bravo did well to keep out.
However, he scored and assisted a goal in the same Barca game for the first time this calendar year and Koeman was pleased with the France international's overall display.
"I hope to see him continue working like this," he said. "To miss opportunities, you have to be there. His character must be highlighted because he is always there.
"He knows perfectly well that he missed a penalty, but the important thing is that he always shows himself and that type of character is important."