The incident-packed clash saw both sides have a player sent off inside the first 20 minutes and Brazil goalkeeper Alisson shown a red card on two occasions only for both to be rescinded after consultation with the Video Assistant referee (VAR).
Ecuador had a goal chalked off and two penalty awards rescinded via VAR, including one in second-half stoppage time.
Casemiro had put Brazil ahead after five minutes when he hammered home from close range after a goalmouth scramble.
Ecuador goalkeeper Alexander Dominguez was red carded after 15 minutes for a reckless challenge, and Brazil fullback Emerson Royal was dismissed five minutes later for a second yellow card following a clumsy tackle.
Five-times world champions Brazil have already qualified for this year’s finals in Qatar along with Argentina, who are playing in Chile on Thursday.
Ecuador are third in the 10-nation South American qualifying standings with 24 points from 15 games.
Uruguay moved into fourth with 19 points after beating Paraguay 1-0 in Asuncion, Luis Suarez getting the winner five minutes into the second half to give new coach Diego Alonso a winning start.
The result keeps Uruguay’s qualification hopes alive and dealt a heavy blow to Paraguay, who sit second bottom of the table with 13 points.
Colombia and Peru, who meet on Friday, are on 17 points.
The top four qualify automatically for the World Cup while the fifth-placed side go into a playoff with a team from the Asian confederation.
Ecuador’s match against Brazil ebbed and flowed but was enthralling throughout, especially in the opening half hour.
Already a goal down, Ecuador’s keeper Dominguez was shown a red card for a neck-high challenge that felled Matheus Cunha on the edge of the box.
But moments later the numbers were even as Brazil’s Emerson Royal, who was shown a yellow card in the first minute for a firm challenge, got a second for a clumsy intervention.
Brazil goalkeeper Alisson looked like he would be the third player sent off after 25 minutes but following a lengthy delay Colombian referee Wilmar Roldan overturned the decision.
Ecuador, on a home pitch where they had earned 16 of their 23 points ahead of Thursday’s match, thought they might snatch all three points when they were awarded a stoppage-time penalty.
Alisson felled Ayrton Preciado in attempting to punch the ball clear and was again shown a red card, but after consulting VAR the referee overturned both the penalty award and red card.
The draw saw Brazil extend their unbeaten run in World Cup qualifiers to 31 games to match the South American record they set from 1954 to 1993.
Bottom side Venezuela are the only team out of the running to qualify for Qatar, with most sides having four games left to play.