A source close to the singer, who spoke on condition of anonymity, said the cancellation was not linked to Bieber's collapse on-stage in London last week, which forced the teen sensation to take a 20-minute break for oxygen and later to visit a hospital.
"Due to unforeseen circumstances, Justin Bieber was forced to cancel the second performance in Portugal, March 12," a statement said on the website of the Pavilhao Atlantico.
"The Canadian singer is eager to play for the Portuguese fans on March 11," it added. Ticket holders for the canceled gig were entitled to a refund if they claimed it within a month.
The Bieber source did not give a reason for the cancellation, but local media in Portugal reported that tickets sales for the March 12 gig, which was added to his itinerary in February, were lower than organizers had hoped.
Bieber described his visit to London as a "rough week".
As well as the collapse, the 19-year-old was caught on film in an expletive-filled altercation with a photographer, showed up nearly two hours late for a show leading to widespread anger and was labeled a "pop brat" by a leading tabloid.
Discovered on YouTube in 2008, Bieber has built an online following of tens of millions of fans and is one of the pop world's biggest stars. In February, he became the youngest artist to land five chart-topping albums in the key U.S. market.
(Reporting by Mike Collett-White; Additional reporting by Andrei Khalip in Lisbon; Editing by Jon Hemming)