The Ligue 1 club triumphed 2-1 to seal a 5-2 aggregate victory and book a quarter-final place but the game was marred by the behaviour of a section of the travelling supporters.
One of the guards, a 57-year-old man, was wounded in the neck by a sharp object but his injuries were not serious and he is in a stable condition, according to Basurto Hospital.
A second member of the security personnel sustained minor hand injuries.
The Bilbao police force tweeted to wish the injured staff – supplied by security firm Prosegur – a speedy recovery.
Additionally, from their position in the second tier of the stadium, Marseille fans lit flares and some fell into the section occupied by Bilbao supporters below.
When Athletic hosted Spartak Moscow during the previous round last month, a police officer died when he suffered a cardiac arrest following violence between rival fan groups ahead of kick-off.