Leonardo Ramos' side took advantage of a slip-up from previous leaders Nacional – who lost 5-3 at Defensor Sporting on Thursday – with their home triumph over the struggling Fenix.
They made an ideal start, scoring inside the first minute thanks to striker Jonathan Alvez, but were pegged back on the stroke of half-time.
Danubio pressed for the goal with a series of attacking substitutions but they left it exceptionally late, with Alvez's second – which came in the fourth minute of stoppage time – proving the difference between the two sides.
Nacional seemed set for victory thanks to Alvaro Recoba's fifth-minute strike but Defensor had other ideas, scoring five times in an incredible final 25 minutes.
Giorgian De Arrascaeta initially levelled proceedings in the 66th minute, before Ignacio Risso fired them ahead from the penalty spot.
Felipe's fourth – quickly followed by another Risso penalty – did the job for the home side, but Gonzalo Ramos still found time to respond in a crazy end to the match.
And also on Sunday, the league's top scorer Hector Acuna grabbed a double as Cerro won 3-2 at El Tanque Sisley, while Cerro Largo edged Racing CM 1-0 thanks to Fabricio Nunez's strike.
