Benegas struck in the 35th minute to give Ariel Pereyra's men the lead at the interval, before he inflicted more damage in the second half at the Estadio CAP.
The Argentine converted from the penalty spot three minutes after the break, before Francisco Bahamondes made it 3-0 moments later.
Benegas wrapped up his hat-trick with 25 minutes to play, making it eight goals in as many games.
The striker is on track to smash his previous best goal tally in a season, having scored 12 in the 2013-14 campaign in 29 appearances.
Union La Calera are fourth (18 points) having gone unbeaten in six matches, while Huachipato are fifth (17) - with second to fifth playing off for the Copa Libertadores places at the end of the Apertura phase.
On Sunday, Santiago Wanderers struck late to secure a 1-0 win at home to Union Espanola.
A 90th-minute goal to Pablo Tamburrini gave the hosts their third straight win, with Espanola unable to find a response in five minutes of additional time.
Wanderers sit third with 22 points, six shy of leaders Universidad Chile, while Espanola reside in sixth (16 points).
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