Former Guadalajara player Ochoa scored after a quarter of an hour when he leaped on to a poor back-pass and twice more in the dying minutes when the Chivas, Mexico's most popular team, were down to nine men in Saturday's match at their Omnilife stadium.
Guadalajara had striker Omar Bravo sent off with a straight red card just past the half hour and Patricio Araujo 13 minutes from time for a second bookable offence.
It was only the second win in eight matches for Chiapas who are bottom of Group Three with nine points.
Cruz Azul notched their fifth win in succession beating Queretaro 3-0 to open a 10-point lead in Group Three with 21 points from eight matches. They are also three points clear in the overall standings.
"The impression is that we've improved, but things don't stop here, we've only played eight fixtures and we've got to be wary," Cruz Azul coach Enrique Meza told reporters.
Argentine forwards Emanuel Villa, with a header, and Maximiliano Biancucchi gave Cruz Azul a 2-0 first-half lead. Adrian Cortes scored the third goal with a free kick in added time.
"The team's winning, playing well and creating chances which is important but we haven't achieved anything yet, we're just on a good run," said Villa.
Santos Laguna, who beat Necaxa 2-1, and Monterrey, who won 2-0 against one-point Atlas, share the lead in Group One with 18 points apiece.
Atlante won for only the second time, 2-0 at home to Morelia, in their first match under new Argentine coach Eduardo Bacas who has replaced the sacked mexican Isidoro Garcia.
Title holders Toluca were at home to America on Sunday with both sides looking to snatch the lead in Group Two from San Luis.
The top two teams in each group and the two next best placed sides on points after the 17-match round-robin stage qualify for the knockout phases.
