The 26-year-old’s first-half double powered Jean-Marc Furlan’s side to their fourth victory this term at Stade de l'Abbe-Deschamps.
Yattara gave Auxerre a 14th-minute lead after profiting from Mickael Barreto’s assist, before making it two goals - four minutes later.
With no goal in the second half, AJA cruised to victory to boost their chances of making a return to France’s elite division.
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The Guinea international was on parade from start to finish, while Benin Republic’s Jordan Adeoti was replaced by Yanis Merdji in the 82nd minute.
Hamza Sakhi came on for Barreto in the tie’s closing stages while Comoros’ Benjaloud Youssouf and Mauritania’s Abdoul Ba were not listed by coach Furlan.
Zimbabwe's Tino Kadewere, Ghana's Ebenezer Assifuah and Senegal's Jamal Thiare were all in action for Le Havre.
With 15 points from 10 matches, Auxerre sit in seventh position on the log. They are guests of fourth-placed Lens on Monday.