The 26-year-old became the first Spaniard to win the Copa Libertadores in November and moves to the Emirates Stadium for the remainder of the 2019-20 season.
Arsenal announced the deal on Tuesday afternoon and the club are thought to have paid an initial loan fee of around £4million and have the option to make the move permanent for an additional £8million.
Mari, who played the whole game for Flamengo as they lost to Liverpool in extra-time of the Club World Cup final last month, becomes the first signing under Gunners head coach Mikel Arteta.
Having travelled to London with Arsenal technical director Edu over the weekend, Mari returned to Brazil with speculation the move had stalled after a disagreement of the terms of the deal.
But the move has gone through and Edu revealed Arsenal have been tracking Mari for some time.
“Pablo is an experienced player who will provide us with additional defensive quality,” he said.
“We have been monitoring Pablo’s career for a while and we are very pleased to have reached agreement with Flamengo for him to join us initially until the end of our season.
“Together with Mikel and his coaching team, we are all looking forward to seeing Pablo in an Arsenal shirt.”
The need to add to his defensive ranks was not lost on Arteta, who has seen Calum Chambers and Shkodran Mustafi sidelined with injuries and Konstantinos Mavropanos leave for Nurnberg on loan.
Mari came through the ranks at Real Mallorca before moving on to Gimnastic and then to Manchester City.
He failed to make a first-team appearance at the Etihad Stadium but would have worked closely under Arteta, who was Pep Guardiola’s assistant at the time.