Mexico needed just to avoid defeat in Recife to take their place in the knockout phase, but three goals in 10 second-half minutes killed off Croatia's hopes.
The Mexicans needed more than an hour to break the deadlock at the Arena Pernambuco before the floodgates finally burst.
Marquez scored with a header on 72 minutes before Andres Guarado grabbed Mexico's second and substitute Javier Hernandez netted a third in quick succession to book their Dutch showdown on Sunday in Fortaleza.
Croatia bow out by finishing third in the group after their opening 3-1 defeat to Brazil and 4-0 trouncing of Cameroon, while Mexico finish second in the table to Brazil on goal difference.
Coach Niko Kovac had recalled defender Sime Vrsaljko for Croatia, with left-back Danijel Pranjic pushing up into midfield, but it was a move that ultimately didn't pay off.
The Mexicans were unchanged from the side that held hosts Brazil to a goalless draw last Tuesday thanks to the heroics of goalkeeper Guillermo Ochoa. Mexico coach Miguel Herrera opted to again leave Hernandez out of his starting line-up before the Manchester United star netted after coming on for the final 25 minutes.
Croatia fired in numerous crosses, but Mexico goalkeeper Ochoa was again solid between the posts. After a goalless first-half, the Mexicans got the breakthrough when Herrera's corner was powered home after Marquez out-jumped the defence on 72 minutes.
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