Santos - which beat Juventude on Wednesday - edges Atletico on winning percentage. Both clubs have 51 points from 28 matches.
Fernandinho put Atletico ahead after coming up with a loose ball inside the penalty area in the 14th minute.
Washington sealed the win - Atletico's third consecutive - with a goal from inside the box in the 80th.
The result kept alive Atletico's 10-game unbeaten streak. The 2001 national champion hasn't lost since July 24.
Guarani winless in nine matches fell to last-spot in the 24-team standings.
Santos remained atop the table after midfielder Ricardinho netted an amazing late game-winning goal in the team's 2-1 victory against Juventude at Alfredo Jaconi Stadium on Wednesday.
Ricardinho recovered the ball near midfield and sent a high lob shot from about 40 meters (yards) away over goalkeeper Eduardo Martini who was just returning to his net after making a save outside the penalty area.
Midfielder Elano had put Santos ahead in the 11th minute and defender Naldo had equalized for Juventude in the 25th.
The result snapped Juventude's eight-game unbeaten streak. The Rio Grande do Sul state team which is in third-place with 48 points hadn't lost since a 2-1 result against Sao Paulo on July 28.
Also Wednesday Cruzeiro suffered an embarrassing 4-1 home loss to minnow Parana at Mineirao Stadium in a result that dropped the defending champion to 13th-place in the standings.
Parana - which has lost 16 of its 28 matches - moved out of last-place with the victory.
Fourth-place Palmeiras had a chance to move closer to the leaders but was held by Ponte Preta to a scoreless draw in Campinas.
At Maracana Stadium veteran striker Edmundo scored a first-half penalty-kick goal to lead Fluminense to a 3-1 win against struggling Internacional.
The result cost coach Joel Santana's job with Internacional which has won only two of its last 13 matches. Muricy Ramalho was hired Thursday as Santana's replacement.
Fluminense remains unbeaten at home with nine victories and five draws.
Sao Paulo winless in three matches fell 3-2 to Coritiba at its own Morumbi Stadium in what was the team's first loss at home in this year's national league.
The three-time national champion playing its first match since top striker Luis Fabiano was transferred to Portugal's FC Porto hadn't lost to Coritiba at Morumbi in 19 years.
Coach Sinval Cuca resigned after the result saying he had given his best "but it wasn't enough anymore."
Sao Paulo rival Corinthians celebrating its 94th anniversary defeated Atletico Mineiro 1-0 at Pacaembu Stadium to jump to eight-position. The three-time champion - unbeaten in three matches - has won four of its last six games.
In other results Thursday Serbian Dejan Petkovic netted a pair of goals as Vasco picked up a 2-1 come-from-behind victory against Gremio in Porto Alegre while Flamengo beat Vitoria 2-0 at Maracana Stadium in what was the team's third win in a row.
In Belem Botafogo lost its first match in four rounds by falling 2-0 to Paysandu.