The Italian, who is understood to be interested in signing the prolific striker, was at the Vicente Calderon to see the 26-year-old head home after just six minutes
The striker, who has been linked with a possible January switch to the Premier League champion or Chelsea, scored after just six minutes, heading in an Emre cross as his side moved level on points with Barcelona at the top of La Liga.
The Colombian has recently indicated his desire to one day play in England, but Atletico chairman Enrique Cerezo is not worried about the future of the prolific 26-year-old, despite being aware of Mancini's presence in Madrid.
"We know that Mancini has come to watch the game but we are calm with the topic of Falcao," Cerezo told Cadena Ser.
"I guess Mancini came here to search for a home in Malaga," he also later joked to Canal+.
Falcao has already scored 11 goals this season, including a breathtaking hat trick against Chelsea in a 4-1 European Super Cup win.
The goals have continued to flood in for the former Porto man, who struck 36 times in all competitions for Atletico during the 2011-12 campaign, his first season with the Spanish side.