Both men did see game time, but not until early in the second half when Barca found themselves trailing.
Messi was able to make a telling contribution, as he provided the assist for El Haddadi Munir’s leveller in a 1-1 draw, but more points slipped through the grasp of the reigning Spanish champions.
Valverde has now seen his side go three games without a win, but has defended his decision to once again rest senior stars, telling reporters: "When I make the decision, I think about what's best for my team and for my club.
"I always do that before playing games, I can't do it afterwards or rewind.
"Fans can decide what they think is convenient, but I need to think about the best for my team.
"It's my absolute responsibility, we have four games in ten days and I thought that Leo and Busquets had to rest knowing that we have a very difficult match on Wednesday.
"I knew it was a risky decision, but if it had gone well, you wouldn't be asking me about it."
It is imperative that they rediscover their spark in that contest, with the club currently enduring their worst run during Valverde’s tenure.
He added: "A difficult week because we have not achieved the objectives.
"But there are things that I think we can improve, above all, our offensive balance."
Barca’s standing at the Liga summit is now under threat, with arch-rivals Real Madrid in a position to overtake them if they can emerge victorious in a derby date with Atletico.