The two men, aged 35 and 39, were picked up in the northern port city of Hamburg soon after the early-morning attack on the regional daily Hamburger Morgenpost Sunday, which caused only minor damage.
Investigators said there was not enough evidence to keep the two in custody for the firebombing, which has an undetermined motive.
"The men denied any connection with the arson attack under questioning by officers from the state security service," Hamburg police said in a statement.
Police said the probe was continuing and that they are still trying to establish whether there was a connection between the German newspaper's show of support for Charlie Hebdo, where jihadist gunmen slaughtered 12 people on Wednesday in Paris, and the firebombing.