Goalkeeper Marc-Andre ter Stegen made some superb saves in the second half and Alex Berenguer struck the post, but Athletic could not break down the league leaders.
When Inaki Williams eventually did late on, the goal was disallowed after VAR spotted a handball by Iker Muniain in the build-up.
With Ronald Araujo suspended, Xavi used Jules Kounde alongside Andreas Christensen and started Sergi Roberto at right-back.
Ferran Torres, starting on the left, pulled a shot narrowly wide of the near post as Barcelona began brightly, still without injured duo Ousmane Dembele and Pedri.
Ernesto Valverde, who won two league titles with Barcelona before he was sacked in 2020 with the team still top of the table, moved Nico Williams over to the left flank to try and get in behind Sergi Roberto.
Athletic pressed well and never let Barcelona rest, the Catalans uncomfortable but staying afloat, despite the absence of key centre-back Araujo.
Lewandowski should have sent Barcelona ahead but took a heavy touch and Athletic goalkeeper Julen Agirrezabala was able to snatch the ball from the striker's toes.
The midfield battle was intense, exemplified by Gavi throwing himself at the ball to try and block a pass with a diving header.
Athletic fans threw fake banknotes with the word "mafia" printed on them into the air, in protest after Barcelona's corruption charge.
On the pitch the Catalans were under the cosh too, with Marc-Andre ter Stegen denying Inaki Williams low at his near post.
Raul Garcia crashed a header off the crossbar from the resulting corner, as Barcelona clung on.
Against the run of play, they took the lead before half-time, when Sergio Busquets cleverly found Raphinha, who finished clinically with his weaker right foot.
The goal was initially flagged offside but VAR showed Raphinha was in a legal position when he received the ball, and soon the Brazilian was able to celebrate.
Raphinha's goal helped Barcelona beat Valencia by the same scoreline last week, and the Brazilian is enjoying his best form since joining from Leeds United last summer.
Backs to the wall
Lewandowski might have doubled Barcelona's lead in the second half but headed wide after a fine run and cross by Alejandro Balde.
Athletic came close to equalising again when Alejandro Berenguer broke in down the left but struck the post.
Ter Stegen made a fine save at full stretch to claw out a Muniain effort from the edge of the box, as Athletic attacked in waves.
Eventually Inaki Williams blasted past Ter Stegen after racing through on goal but Athletic were left infuriated after Muniain's handball was spotted at the start of the move.
In stoppage time Los Leones had another fine chance as the ball bounced around in the box but Ter Stegen produced another superb save and Marcos Alonso blocked another goal-bound effort, to secure Barcelona's victory.
It leaves the Catalans sitting comfortably clear ahead of next Sunday's Clasico at Camp Nou.