Guadalajara, the country's most popular club, are the only team with maximum points after two rounds after their 3-1 away win over Tigres UANL in Saturday's action.
Pumas UNAM, winners of last year's Clausura, are one of three teams with four points after their 0-0 draw away to Cruz Azul, who are also unbeaten on four points.
"It was something unforgettable, I had a lot of luck today. This gives you confidence because it's the start of the tournament," the 33-year-old Zepeda, who came back last year from almost two seasons out of first division football, told Televisa.
Atlas, under new Argentine coach Carlos Ischia, went ahead after 19 minutes with a fine goal by Zepeda.
Despite his slight build at 1.65 metres, he beat burly defender Jose Basanta to a long ball from Edgar Pacheco and placed it past advancing keeper Jonathan Orozco.
Former Mexico international Zepeda struck again three minutes after halftime with a header from a corner by Argentine Dario Botinelli.
He completed his hat-trick in the 65th with a header at the far post after Orozco misjudged a cross from Uruguayan Gonzalo Vargas.
Monterrey had defender Severo Meza sent off in the final minute for a bad foul on Atlas substitute Hebert Alferez.
SECOND DOUBLE
Striker Javier Hernandez scored twice for Guadalajara to take his tally to four goals in two matches, his opener a header after only two minutes after Omar Bravo had flicked on a cross from midfielder Xavier Baez.
Hernandez lobbed goalkeeper Cirilo Saucedo for his second in the 26th, defender Jesus Molina pulled one back and full back Hector Reynoso made it 3-1 before half-time.
Mexico striker Miguel Sabah also scored twice as Morelia won 2-0 at home to America, who had begun the tournament with a 5-1 rout of San Luis last weekend.
San Luis recovered to upset CONCACAF Champions League title holders Atlante 3-2 away in Cancun on the Caribbean coast with two goals from 35-year-old midfielder Braulio Luna.
Atlante's new Peruvian signing Johan Fano hit both the home side's goals in the space of four minutes to give them a 2-1 half-time lead.
