The deal for Pablo is worth up to £12m, with Arsenal paying an initial £4m loan fee upfront while having the option to make the move permanent for £8m in the summer.
The 26-year-old has established himself as one of the best defenders in South America since his move to Brazil in July 2019.
During the last South American season, Pablo won the Brazilian Serie A title and Copa Libertadores with Flamengo, under the tutelage of head coach Jorge Jesus.
The Spaniard was on the books of Manchester City in 2016 when Mikel Arteta was working as an understudy to Pep Guardiola.
Pablo becomes the first signing of the Spanish coach since he became the manager of the Gunners.
He had three successful different season-loan spells during his time at Manchester - in Spain with Girona for the 2016/17 season, then to the Netherlands with NAC Breda in 2017/18, before returning to Spain for the 2018/19 campaign with Deportivo La Coruna.
Arsenal technical director Edu said Pablo will be an addition of quality to the North Londoners defensive unit.
“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.”