The 31-year-old Italian has been by Nibali's side since 2008 in the colours of Liquigas, and followed him to Astana in 2013. He has served as a domestique to the Sicilian at five Grand Tours, including both Giro d'Italia triumphs – in 2013 and 2016.
"I have to thank Nibali, who wanted me to be involved in this new team together with him," said Agnoli in a statement from the team.
"Between us the cycling relationship is a minimal part, because we are above all true friends, also with our families, and we trust each other. I'll give 1,000 per cent not to let him down. As usual I will be happier for a success of Vincenzo, than for my personal result. I'll give everything for him."
Agnoli has spent his career working for others, and only has one professional victory to his name – at the 2005 Tour of Qinghai Lake – excluding team time trial victories with Liquigas at the 2010 Giro d'Italia and with Astana at this year's Giro del Trentino - where he wore the leader's jersey as a result.
He brings Grand Tour experience, having ridden nine Grand Tours, including seven of the last eight editions of the Giro.
"Having Valerio on the team signifies having a stamp of guarantee as an asset for the team – he is one of the most loyal teammates in the peloton, a classy rider who will help wherever and always delivers what is asked of him," said team manager Brent Copeland.
"The thing with Valerio is that you have the perfect combination of loyalty together with experience, and mixing these qualities together into one rider only bears good fruit for the team in general. Myself and the team's technical staff are very pleased to have him as being part of the team."
The signing of Agnoli sees the Bahrain-Merida roster continue to take shape, with the newly-formed team hoping to secure a WorldTour licence for 2017.
The team has also signed Ivan Garcia Cortina (Klein Constantia), Enrico Gasparotto (Wanty Groupe Gobert), Giovanni Visconti (Movistar), Manuele Boaro (Tinkoff), Kanstantsin Siutsou (Dimension Data), Borut Bozic (Cofidis), Sonny Colbrelli (Bardiani-CSF), Luka Pibernik (Lampre-Merida), Heinrich Haussler (IAM Cycling), Grega Bole (Nippo Fantini), Chun Kai Feng (Lampre-Merida) and Niccolò Bonifazio (Trek-Segafredo). Further announcements are expected in the coming weeks and months.