For the second time in the tournament, the Reds full-back was an unused substitute, while ex-United defender Daley Blind was selected on the left side by the club's former manager Louis van Gaal.
The Dutch boss did bring on four substitutes as the second half unfolded in Doha, sending on another Old Trafford alumnus, Memphis, from the restart.
But Malacia was not among the deployed replacements and therefore watched the full game from the bench, just as he did when his national team beat Senegal 2-0 in their opener.
Going into the game as Group A leaders, the Netherlands would have been the first nation to book a place in the last 16 if they had beaten Ecuador at the Khalifa International Stadium, following Senegal's 3-1 triumph over the hosts Qatar earlier in the day.