The Heat stopped publication last month after the Home Ministry suspended it, saying it had violated its printing permit and failed to respond to the ministry to explain the matter.
Fifty journalists and activists, wearing red and chanting "free the media", held an hour-long protest in the capital, where they urged the government to lift the suspension and stop controlling the press.
"This is not just about the suspension of The Heat. It's about the freedom of the press," activist Ambiga Sreenevasan said.
"It is about fighting for the rights of the people, the rights of the people to speak and to receive information."
The Heat, which was launched last year, denied that it had not not responded to the letters the ministry sent to it in late November and early December.
Home Minister Zahid Hamidi was quoted by local media on Monday as saying that the suspension was "temporary".
The Heat on its website describes itself as "a weekly that intends to push the boundaries of press freedom" with investigative stories on social, economic and other current issues.
The suspension followed an article on Prime Minister Najib Razak's "growing expenditure" on overseas trips and other expenses.
Mr Najib's 56-year ruling coalition, which was re-elected in May with its poorest showing yet, dominates mainstream media through permits and ownership linked to political cronies.
During the election campaign last year, mainstream newspapers and TV barely acknowledged the existence of the opposition led by Anwar Ibrahim.
But criticism of the regime is flourishing online on news portals and social media sites.
Amid pressure, Mr Najib has vowed to grant greater civil liberties, loosening decades-old security and other laws deemed repressive by critics.
But he is facing resistance, including from his own party members used to decades of iron-fisted leadership, and critics accuse him of mere window-dressing to gain votes.