Cameras surrounding Luzhniki stadium in Moscow showed some Moroccan fans crying after the game.
Portugal face Iran in their final group game on June 25 in Saransk.
Morocco continued to control possession as the second half got underway, and almost had their equalizer in the 57th minute, only for Rui Patricio to come up with a stunning save from Belhanda's header.
Twice they went close before the hour through Younes Belhanda, the forward's second effort - a bullet header towards the corner - brilliantly saved by Rui Patricio.
Their first match, against Spain, ended in a wild 3-3 draw with Cristiano Ronaldo scoring a hat-trick, but while Santos was pleased with some aspects of that game, he expects his team to improve in certain areas.
Ronaldo's fourth-minute goal moved him past the legendary Ferenc Puskas onto 85, and now only Iran's Ali Daei has scored more worldwide goals (109) than the Real Madrid forward. He could not get the ball up and over a solid wall of defenders on either occasion.
The Real Madrid player, who won his fifth Champions League crown last month, now has 85 worldwide goals - a record for a European player. His hard tackles from behind, however, earned him a yellow card.
Morocco's forward Noureddine Amrabat reacts at the end of the Russian Federation 2018 World Cup Group B football match between Portugal and Morocco at the Luzhniki Stadium in Moscow on June 20, 2018.
Portugal is in Group D of this year's tournament alongside Spain, Morocco and Iran.
After struggling and ultimately failing to break down Iran's defence last time out, Morocco will do well to turn on the style and test Portugal in this fixture, now playing against far superior opposition in the 2016 Euros winners. It wasn't the greatest showing from the Portuguese, as Morocco controlled possession and created more chances, but the finishing was abysmal.