Midfielder Sofiane Boufal, a former Southampton star, but now playing with Al Rayyan in Qatar, gave Morocco the lead after 29 minutes, scoring with a powerful turn and drive from a pass by Bilal El Khannous, the AFP reported.
Brazil skipper Casemiro levelled in the 67th minute when his weak shot was fumbled by goalkeeper Yassine Bounou.
But on-loan Sampdoria midfielder Abdelhamid Sabiri struck the winner with a volley in the 79th minute as Morocco showed that becoming the first Arab or African nation to reach the World Cup semi-finals last year was no fluke.
Before kick-off at the Ibn Batouta stadium, both teams paid tribute to Pele, who died last December at the age of 82.
Until Saturday, Morocco had suffered defeats in their only two other meetings with Brazil -- 2-0 in a 1997 friendly and 3-0 in the group stages of the 1998 World Cup in France.
MNA/PR