Porto said they had "reached an agreement for the end of the contractual agreement" with Peseiro, who replaced Julen Lopetegui, himself sacked after only one-and-a-half seasons.
Peseiro, who has also coached teams in Greece, Romania, Saudi Arabia, United Arab Emirates and Egypt, arrived with Porto in third place and was unable to improve on that as they finished 15 points behind champions and arch-rivals Benfica.
Porto won the Portuguese league nine times out of eleven between the 2002 and 2013 but have seen Benfica walk off with the title in each of the last three seasons.
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Peseiro was the ninth man to coach the 27-times Portuguese champions in the last 12 seasons since the departure of Jose Mourinho.
"They were only a few months, but of great work and dedication in the interests of Porto," Peseiro said in a statement.
"Myself and the coaching staff did everything we could to be worthy of this club and bring happiness to the fans. Unfortunately, for various reasons, we couldn't give it to them."
The high point of Peseiro's spell in charge was a 2-1 win at Benfica.
However, his side suffered embarrassing league defeats to smaller teams such as Tondela and Pacos de Ferreira, and were knocked out of the Europa League by Borussia Dortmund at the Round of 32 stage.
They ended the season by losing the Portuguese Cup final to Braga, who won on penalties after a 2-2 draw.
(Writing by Brian Homewood; Editing by John O'Brien)
