Consumer advocacy group Public Knowledge blasted the move, accusing Viacom of using Internet users as "a pawn in its negotiations."
On Monday's show, Stewart said the Internet blackout would likely just cause many viewers to download his show illegally.
"This morning, when I woke up, my 8-year-old son was watching Dark Knight Rises [which doesn't open in theaters until July 20] in 3D. They're already figuring it out," Stewart said. "So basically you're blocking old people from watching the show, and just giving people a chance to discover that there's other entertaining s--- in the world."
In a blog post announcing that the shows would again be available online, Viacom noted that Stewart had wasted "no time in weighing in on" the contract dispute.
" 'The Daily Show' continues to exercise the creative and editorial freedom that makes it consistently great," the company wrote.
Public Knowledge said Viacom did the "right thing" by putting its shows back online.
"The biggest fans of shows tend to seek them out online, and it makes no sense for networks to punish them," John Bergmayer, an attorney for Public Knowledge, said in a statement. "Access to online programming is in the interests of viewers and networks alike."
The Senate Commerce, Science and Transportation Committee is set to hold a hearing next week to examine the 20-year-old law governing cable television. Chairman Jay Rockefeller (D-W.Va.) said he wants to find a way to protect viewers from carriage disputes, like the one between Viacom and DirecTV.
"In particular, I want to take a close look at how we make sure that consumers do not continue to get caught in the crossfire in programming disputes, facing dark screens and losing access to news, sports and other entertainment programming,” Rockefeller said in a statement.