The Paris St Germain striker saw his first attempt saved but was allowed to retake the kick after the referee spotted movement before the ball was struck.
Brazil were the better side for most of the match, but struggled to break down a plucky Ecuadoran side who had won three of their previous four qualifiers.
Flamengo's Gabriel Barbosa, making his first international start in five years, had a goal disallowed for offside three minutes before half time and moments later Dominguez scooped a low drive from Neymar round the post.
The result means Brazil are top of the 10-team South America group, with 15 points from five games, four ahead of second-placed Argentina. Ecuador are third with nine.
The top four teams in the section qualify automatically for Qatar 2022 and the fifth-placed side goes into an intercontinental play-off.