The No.8 seed from Estonia overcame Barbora Krejcikova in her opening match and became the first player to reach the semi-finals in Guadalajara by racking up a career-best 12th straight win in just 57 minutes.
Pliskova was victorious in each of the pair's previous three meetings and applied some early pressure but was unable to convert any of the three break points she engineered in game three of the opening set.
Kontaveit, meanwhile, pounced on her first opening, showing the clinical touch that has seen her pick up recent titles in Moscow and Cluj-Napoca with a winner to take the set.
The world No.8 reeled off the next six games to guarantee a top-two finish in Group Teotihuacan and secure a tour-leading 38th hard-court match win this year.
Pliskova could yet salvage a place in the semi-finals by overcoming Barbora Krejcikova in her final round-robin match, though.