Santos paired Nani with Cristiano Ronaldo in a fluid attacking system and both players were on target as Portugal raced into a 2-0 lead before half-time, although Romelu Lukaku grabbed a goal back for the world's top-ranked side after the interval.
Portugal's coach said he feared a repeat of Friday's shock 1-0 loss to Bulgaria - in which Ronaldo had a penalty saved - after Thibaut Courtois made a series of fine early saves, before Nani opened the scoring with a cool finish.
"In the first 10 minutes I thought it was going to happen, the same thing we saw against Bulgaria," Santos said.
"Courtois made two or three fantastic saves. In the first part we again make a good game, facing a very strong team as Belgium. We had always controlled the game, with some possession of Belgium, but nothing that caused us major problems.
"The second half was different, also with good control, but there was a time we break a little. In the game with Bulgaria did not do anything wrong, there were good things, but today also we did all right.
"We must continue to work, work, work."
Belgium coach Marc Wilmots bemoaned the poor start made by his side, although they were without key players including Jan Vertonghen, Vincent Kompany, Eden Hazard, Kevin De Bruyne and Christian Benteke.
"We played too slowly in the first half," said Wilmots. "We have not sought enough depth. We were too late in repositioning, too much space was left. We sometimes ran behind the ball, it is wrong.
"But I've learned some positive lessons from this meeting. [Thomas] Vermaelen is not in his place at left-back.
"There has been positioning problems but later, we went to a 4-4-2 system that has worked better.
"We were seeking higher [positions] in the second period, it worked, it is positive."
