The 33-year-old Leinster lock has numbered among Joe Schmidt's most trusted lieutenants, starting 50 of the Kiwi head coach's 67 Test matches as Ireland boss.
But Jean Kleyn has been given the nod ahead of Toner, with boss Schmidt selecting Munster's South Africa-born star alongside Iain Henderson, James Ryan and Tadhg Beirne in a four-strong lock cordon.
Kleyn only qualified for Ireland on residency two days before his Test debut, the 29-10 victory over Italy on August 10.
Now the 26-year-old has edged out Toner, who has proved a lineout and restart banker throughout Schmidt's six years at Ireland's helm.
"To go from 40 players down to 31 was really difficult, but we had a process whereby we looked back through every training, looked through the games," said head coach Schmidt.
"There were some guys who obviously had more experience and probably had more credit in the bank and were more established and there were other guys who were trying to force their way into the group, and trying to get a balance of current form versus previous performance, it's always a very, very difficult conundrum to solve."
Munster's Chris Farrell has forced his way into Ireland's four-strong centre ranks ahead of Ulster's Will Addison, with Bundee Aki, Robbie Henshaw and Garry Ringrose also present.
Rory Best continues as captain as expected, the 37-year-old Ulster hooker already boasting 119 caps.
Leinster's Luke McGrath has edged out Kieran Marmion at scrum-half, with Ireland taking just two recognised nines to Japan.
Fly-half Joey Carbery will cover scrum-half as an emergency option, with Schmidt taking three 10s.
Jack Carty has won selection ahead of Ross Byrne as Ireland's third playmaker, with Andrew Conway earning a place among a five-strong back-three group.
Carbery is recovering from an ankle problem but Ireland insist he will be ready for the Pool A kick-off, against Scotland in Yokohama on September 22.
Johnny Sexton suffered a thumb sprain at the start of the summer and has since carried a minor leg bump, but Schmidt insisted after Saturday's 22-17 win over Wales in Cardiff that the British and Irish Lions star was fully fit.
Ireland hope Sexton will be able to prove his fitness in their final World Cup warm-up match, Saturday's return clash with Wales in Dublin.
Ireland squad for Rugby World Cup
- Rory Best (CAPTAIN, Ulster) 119 caps
- Tadhg Beirne (Munster) 8 caps
- Jack Conan (Leinster) 15 caps
- Sean Cronin (Leinster) 69 caps
- Tadhg Furlong (Leinster) 35 caps
- Cian Healy (Leinster) 90 caps
- Dave Kilcoyne (Munster) 30 caps
- Iain Henderson (Ulster) 47 caps
- Jean Kleyn (Munster) 2 caps
- Peter O’Mahony (Munster) 59 caps
- Andrew Porter (Leinster) 17 caps
- Rhys Ruddock (Leinster) 22 caps
- James Ryan (Leinster) 18 caps
- John Ryan (Munster) 20 caps
- Niall Scannell (Munster) 16 caps
- CJ Stander (Munster) 32 caps
- Josh van der Flier (Leinster) 18 caps
- Bundee Aki (Connacht) 19 caps
- Joey Carbery (Munster) 19 caps
- Jack Carty (Connacht) 6 caps
- Andrew Conway (Munster) 15 caps
- Keith Earls (Munster) 77 caps
- Chris Farrell (Munster) 5 caps
- Robbie Henshaw (Leinster) 37 caps
- Rob Kearney (Leinster) 91 caps
- Jordan Larmour (Leinster) 15 caps
- Luke McGrath (Leinster) 13 caps
- Conor Murray (Munster) 73 caps
- Garry Ringrose (Leinster) 23 caps
- Jonathan Sexton (Leinster) 83 caps
- Jacob Stockdale (Ulster) 20 caps