The teams from the Buenos Aires suburb of Avellaneda went into the derby in crisis mode after each suffered three-goal defeats last week.
Independiente, officially at home but playing at Huracan while their own stadium undergoes renovation work, went ahead in the third minute when Lucas Pusineri was able to head in after being given too much room at a free kick.
Daniel Montenegro added the second from a penalty in the 65th minute after Ismael Sosa was upended by Gabriel Mercado.
The win should safeguard Independiente coach Miguel Angel Santoro's job and will increase the pressure on his Racing counterpart Juan Manuel Llop.
Racing are 16th out of 20 in the relegation standings, which are decided over three full seasons, one position above the danger zone.
Independiente and Racing are traditionally two of the country's most powerful clubs but both have suffered an alarming decline in the last decade.
Their stadiums are situated within 200 metres of each other and they share one of the bitterest rivalries in South America.
Newell's Old Boys, coached by former Argentine international Roberto Sensini, lost their 100 percent record when they were held 1-1 at home by Gimnasia-Jujuy on Friday.
Juan Arraya put the northerners ahead in the 69th minute and Paraguayan Santiago Salcedo equalised six minutes later.
