The Bergamaschi followed their 1-0 win over Palermo with a 2-1 victory at Lecce on Wednesday to wipe out their six-point deduction.
Atalanta, who gained promotion to the top flight last season, were docked six points at the start of the campaign after a match-fixing investigation this summer.
"Now we see the standings from a different perspective," said Atalanta striker German Denis, who scored twice against Lecce. "Finally we have taken away the negative sign.
"It's not that now we can relax and take it easy but at least we can breathe better."
Two wins and a draw in their three matches so far have lifted Stefano Colantuono's side to 17th in the standings.
Atalanta's unbeaten run will be put to the test by a Novara side that travel to Bergamo on the back of their impressive 3-1 midweek win over Inter Milan.
The result was Novara's first victory of the campaign and handed Attilio Tesser's side a huge morale boost ahead of this weekend's encounter.
"It's our first win and they are three very important points," Tesser said.
"To win against one of the most prestigious teams in Italy makes it all the more special.
"I'm sure this win will give my players a lot of confidence and belief."
The hosts will be without defender Stefano Lucchini, who suffered a muscular injury in midweek and has been ruled out for at least a month.
Tesser is poised to name an unchanged side from the team that beat Inter on Tuesday.