Wednesday's results left all three teams on 10 points but Flamengo (+6) and LDU Quito (+4) pipped Penarol (+2) on goal difference.
River Plate progressed to the Copa Libertadores knockout stage after a win at Palestino.
Boca Juniors scored four goals against Jorge Wilstermann on Wednesday, after Cruzeiro's Fred celebrated a first-half hat-trick.
Gremio only have one point from three Group H fixtures following Thursday's 1-0 loss away to Universidad Catolica.
Playing behind closed doors at the Monumental, River Plate were held by Palestino in the Copa Libertadores.
Defending champions River Plate snatched a last-gasp draw at Alianza Lima on Wednesday.
We assess the leading candidates for glory and the potential stars ahead of the start of the 2019 Copa Libertadores.