The Catalans' unbeaten run in La Liga this season looked to be coming to an end at the Ramon Sanchez Pizjuan until Luis Suarez and Messi scored in the 88th and 89th minutes to salvage a 2-2 draw.
Messi had only come off the bench in the 58th minute, having missed both of Argentina's friendly matches during the international break with a muscle problem.
Valverde says he always intended to get the 30-year-old involved against Sevilla but admits his match-saving cameo came despite him not being fully recovered.
"I had planned to bring on Messi anyway," the coach told Movistar. "He's injured but he's been inactive for a while and we thought it would be better for him to play to get some rhythm of competition.
"He was decisive. We think he'll be okay for Roma [on Wednesday]."
Sevilla deservedly went 2-0 up through Franco Vazquez and Luis Muriel, before spurning a host of chances on the counter-attack prior to Barca's late revival.
Valverde concedes his side played a risky game in the second half, adding: "The first half was fairly balanced, even though they had some dangerous counter-attacks. They pressed us high.
"In the second half, they were comfortable with that situation, because they have quick players like [Jesus] Navas. They got the second goal and we had to take a chance.
Messi really likes scoring against certain teams! pic.twitter.com/78XhY4SBz0— Goal (@goal) March 31, 2018
"Usually, we're a team that doesn't concede a lot. The fact we conceded the second goal made us go further forward. We had to take risks and, when you take risks, you know they can get at you."
The draw puts Barca 12 points clear of Atletico Madrid at the top, having played a game more, but Valverde insists the title race is not yet over.
"We don't think the league is won," he said. "Not at all. That's why we compete until the end. It shows the spirit of the team and that's why we're celebrating like this."