The Canadian wildcard suffered a rocky tiebreaker in the first set, losing her serve three times, which handed her Spanish opponent a 7-6 (7/3) advantage.
But Marino, who came back from an extended hiatus in 2017, regained her composure and fought back in the second set, breaking Garcia Perez three times on her way to 6-2.
The unseeded Spaniard returned fire, taking the opening three games of the third set, but lost her serve twice as Marino levelled up in the seventh game then pulled ahead in the ninth before winning 6-4.
The victory sees her progress to the quarter-finals where British number three Watson awaits after her second round win over Annie Leylah Fernandez.
In other action, Sofia Kenin of the US booked a quarter-final with number three seed Monica Puig of Puerto Rico.
The fifth seed defeated wild card Francoise Abanda 6-4 6-4, two years after the 19-year-old American lost to the Canadian.
Croatian number two seed Petra Martic also progressed with a dominant performance over Belorussian Olga Govortsova, beating her 6-0 6-2 in one hour, eight minutes.
She will play American qualifier Jessica Pegula, who overcame Tunisian Ons Jabeur 7-6 (7/3) 6-4, while number eight seed Pauline Parmentier will meet Varvara Lepchenko of the US in the quarters.
Elsewhere top seed Shuai Zhang overcame home favourite Nao Hibino to advance into the Japan Women's Open quarter-finals.
Hibino, the last Japanese player left in the tournament in Hiroshima, broke twice in the first set as she went 4-1 up before China's Zhang fought back and claimed a 6-4 7-6 (7/4) victory.
She will now face the sixth seed and defending champion Zarina Diyas. Kazakhstan's Diyas came from behind to defeat Ukrainian Kateryna Kozlova 6-7 (3/7) 6-2 7-5 in their second-round match.
Second-seeded Su-Wei Hsieh of Chinese Taipei made the last eight with a 6-3 6-2 win against Luxembourg's Mandy Minella, while Zhang's compatriot Qiang Wang, the fourth seed, beat Luksika Kumkhum of Thailand 7-5 6-3.
Wang's quarter-final opponent will be eighth seed Magda Linette after she beat Tamara Zidansek, while Anna Karolina Schmiedlova also got through, triumphing against Viktorija Golubic.
