On Saturday, Van Aert had finished third in the opening time trial and was frustrated not to win a stage for the second consecutive day.
However, he took the overall leader’s red jersey by virtue of six bonus seconds.
“Of course, I wanted to win this stage,” he said.
“My team did a really good job to make it a bunch sprint so it’s unfortunate to arrive second, but today I knew that finishing in the first three meant the red jersey, so after all it’s a good day.”
Several riders were involved in a crash inside the last 4km.
Ineos Grenadiers’ Welsh rider Josh Tarling was lucky to avoid serious injury as he crashed into a wall. All of those involved managed to reach the finish line and did not lose time.
Stage three will take place on Monday and will see the athletes ride 191.2km from Lousa to Castelo Branco.