Goals from Niko Bungert, an own goal from Marwin Hitz and Johannes Geis gave Thomas Tuchel's side their first win in three games.
The first half was evenly contested with Mainz's record signing Koo Ja-cheol starting against the team where he spent 18 months on loan.
Mainz took the lead in the 23rd minute with Geis' corner finding the head of defender Bungert who made no mistake from the near post.
Augsburg suffered some injury issues and were forced into two substitutions inside seven minutes just past the hour mark with Ragnar Klavan and Tobias Werner leaving the field.
It pinched some momentum away from the Bavarians who conceded a second in the 38th minute.
Eric-Maxim Choupo-Moting was the creator, setting up Nicolai Muller who put enough pressure on Matthias Ostrzolek only for the defender to smash the ball against Hitz's face and send the ball into the net.
Former Augsburg midfielder Koo, also the captain of the South Korea national team, was desperate to score against his old side and he came close twice after the break.
Firstly, he headed wide from Geis' corner in the 54th minute and then a few seconds later was denied by an excellent stop from the Augsburg goalkeeper.
Mainz made the three points safe with eight minutes remaining through their impressive German midfielder Geis who struck sweetly from 30 yards out.
Tuchel's side keep pace with Bayer Leverkusen and Wolfsburg for the remaining Champions League spot and occupy one of the Bundesliga's Europa League slots.