Ernesto Valverde seemingly had one eye on Wednesday's Champions League trip to Tottenham considering his decision to leave Messi in reserve, but he came on to set up Munir's late equaliser and at least prevent Barca losing a second consecutive match.
Although Barca played some neat football at times in the first half, Athletic posed the greater danger going forward and deservedly went ahead just before the interval through Oscar De Marcos.
Messi finally entered early in the second period and he – like Philippe Coutinhobefore him – struck the frame of the goal late on, before picking out fellow substitute Munir six minutes from time to secure a share of the spoils.
Athletic looked the bigger threat in the first half, with Inaki Williams sending a dipping half-volley just wide after racing in behind the defence to give Barca their first scare 12 minutes in.
Williams troubled again soon after, but he failed to apply the finish under pressure from Arturo Vidal after skipping past Marc-Andre ter Stegen.
Luis Suarez forced Unai Simon into a save from a tight angle in the 37th minute, but Athletic capitalised a few moments later – De Marcos steering Markel Susaeta's cross in after escaping the attentions of Jordi Alba.
Valverde waited nine second-half minutes before introducing Messi and that seemed to boost Barca, with Coutinho striking the crossbar with a volley just past the hour.
Barca's luck looked to have run out when Messi blasted against the post from 12 yards out 13 minutes from the end.
But their talisman kept plugging away and found Munir in the 84th minute with a low cross, the forward prodding past Simon to salvage a point.
What it means: Messi dependency is real
In theory, Barca had more than enough ability in their starting XI to deal with an Athletic side that has not won since their opening match of the season. Yet, before Messi's introduction, the visitors were the more threatening in attack and deservedly had a 1-0 lead. Were it not for Williams' occasionally suspect decision making, it could have been a more impressive half-time lead. Messi was the only one, alongside Suarez, who played with purpose and focus – Valverde should be concerned by that.
