The hosts made a flying start at the Gewiss Stadium, taking the lead inside three minutes when Nikola Krstovic sent Franck Kessie through on goal. Kessie kept his composure to lift the ball over goalkeeper Filip Stankovic.
Atalanta doubled their advantage soon afterwards as Krstovic headed home Eljif Elmas' corner to put the hosts firmly in control.
Stankovic prevented Charles De Ketelaere from adding a third, but the goalkeeper was beaten again in the 30th minute. He parried Jonathan Rowe's effort into Krstovic's path, allowing the striker to score from close range and complete his brace.
Venezia responded before half-time when Antoine Hainaut headed Richie Sagrado's cross into the net, giving the visitors hope of a comeback.
Atalanta remained dangerous, with Davide Zappacosta firing wide before the break, but Venezia returned for the second half determined to reduce the deficit.
Hainaut helped create another opportunity, delivering a cross that Akor Adams headed towards goal. Thomas Kristensen deflected the effort over the bar to preserve Atalanta's two-goal cushion.
Kike Perez then tested goalkeeper Marco Carnesecchi from distance, while John Yeboah used his pace to break through the Atalanta defence. However, Yeboah's effort went straight at Carnesecchi.
Atalanta also threatened to restore their three-goal lead, with Krstovic denied by Stankovic as the hosts looked to put the result beyond doubt.
The closing stages became more complicated for Atalanta when Elmas was sent off for a studs-up challenge on Thorir Johann Helgason. Despite being reduced to 10 men, they comfortably managed the final minutes to secure three valuable points.
The victory lifts Atalanta to nine points and ends a run of three consecutive league defeats. They have now gone eight Serie A meetings without losing to Venezia, winning seven and drawing one.
Venezia, meanwhile, remain bottom of the table with no points from their opening six matches.
Atalanta will look to build on the result when they host Pafos in the UEFA Conference League on Thursday.