Peralta missed the club's 0-0 Liga MX season opener last Saturday against Leon through what was reported as sinusitis.
"After carrying out COVID-19 tests last week as the protocols indicate, Oribe Peralta came back negative," read a statement. "However, he showed symptoms over the weekend.
"Because of that, the club proceeded to isolate and carry out a couple more tests on the footballer. The second test also came back negative, but the symptomatology continued to be present, which meant a third test was applied, which came back negative [on Tuesday]."
The statement added that the 36-year-old Peralta had some "complicated days," but didn't need oxygen and is now in better health and being looked after by the club's medical staff.
There have been multiple cases of the virus at Chivas, whose coach Luis Fernando Tena was confirmed to have the coronavirus on July 15 and wasn't on the bench for last weekend's game.
Liga MX has been shaken by positive coronavirus cases amongst players and staff, with over 100 since the start of the pandemic.
Two games were postponed last weekend while clubs awaited test results, but were played over Monday and Tuesday.
The players that test positive are isolated and only allowed to rejoin the squads when they have a negative result.
The second round of matches in the "2020 Guard1anes" season begins on Friday with Puebla taking on Cruz Azul. The league announced on Tuesday that Saturday's game between Atlas and Pumas would be postponed until Monday due to the delay in testing results.
Cruz Azul midfielder Rafa Baca urged league authorities and fellow players to be transparent and honest to try to reduce the number of cases moving forward.
"For our part, we try to be transparent," said Baca in a press conference Wednesday. "Obviously, when the positive cases went out [in Cruz Azul] it was a big scandal, but I prefer it that way, that they tell the truth, because hiding it could cause more infections, not just inside the club, [but also] in our loved ones, people who are most vulnerable and I think that is what we have to work on."