De Ketelaere scored two goals on Sunday and African player of the year Ademola Lookman grabbed the other as Atalanta restored their two-point advantage over Napoli, who had put the home team under pressure with a 2-1 win over Genoa the day before.
Empoli forward Lorenzo Colombo stunned the hosts with the opener in the 13th minute after a quick throw in caught the Atalanta defence off guard.
Atalanta suffered another blow minutes later when Mateo Retegui had to go off with what looked like a left thigh injury. Nicolo Zaniolo went on for the Italy forward and was booked almost straight away.
Gian Piero Gasperini's side showed no alarm, however, and De Ketelaere equalised with a diving header inside the left post in the 34th.
Lookman then scored his ninth league goal of the season just before the interval after Zaniolo laid off a cross from De Ketelaere.
Sebastiano Esposito pulled one back with a penalty awarded after a VAR check for an innocuous-looking challenge, but De Ketelaere sent the home fans wild in the 86th minute when he fired inside the right post from the edge of the penalty box despite facing three defenders.
Atalanta won the Europa League last season but have never won Serie A. They achieved their highest finish of third place three times under Gasperini.
Juventus ended a run of four straight draws in the league with a hard-fought 2-1 win at relegation-threatened Monza.
Nicolás González scored what proved to be the winner from close range in the 39th minute after Samuele Birindelli had cancelled out Weston McKennie's opener for the visitors.
While Juve remain the only unbeaten team in the league, another draw would have lost them further ground on the leading teams. Juventus have drawn 10 of their 17 games so far and remain nine points off the pace.
Monza dropped to the bottom after their 10th game in a row without a win.
Paulo Dybala scored twice and set up another goal to get Roma back on track with a comfortable 5-0 win over Parma.
The Argentine playmaker scored an early penalty and pounced on a rebound from Alexis Saelemaekers' initial shot early in the second half to steer Roma to just their fifth league win of the season.
Saelemaekers scored with a volley after Dybala's opener, and Leandro Paredes added another penalty in the 74th, awarded after Saelemaekers was shouldered off the ball.
Dybala set up Artem Dovbyk to complete the scoring late.
Roma looked to have finally clicked under Claudio Ranieri, the team's third coach of the season, when they managed back-to-back wins over Lecce and Sporting Braga in the league and Europa League. But they lost last weekend at promoted Como 2-0.
Also Sunday, Venezia defeated Cagliari 2-1 thanks to Marin Šverko's persistence. The Croatian defender kept going despite the attention of a handful of Cagliari defenders to score what proved to be the winner. It lifted Venezia off the bottom, three points above Monza.
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