The defender has signed a contract with the Club until 2020.
A Belgium international, Toby came through the ranks at Ajax, making 186 appearances and scoring 15 goals during nine years with the Eredivisie champions, where he lifted three league titles and one Dutch Cup.
He was named Ajax Talent of the Year in 2010, an honour also won by Jan Vertonghen and Christian Eriksen during their times in Amsterdam.
Toby joined Spanish side Atletico in 2013 and was part of the squad that won the La Liga title on the last day of the season as well as reaching the Champions League final in the same year.
He made 22 appearances in all for Diego Simeone's side, scoring twice, before impressing on loan at Southampton last season. He played 28 times for the St Mary’s club in all competitions, scoring once.
Capped by Belgium at every level from Under-15 to Under-21, Toby made his senior international debut in 2009 and appeared at the 2014 World Cup finals in Brazil, joining Nacer Chadli, Mousa Dembele and Jan Vertonghen in the squad.