The 19-year-old defender spent part of the last campaign on a temporary deal at Oldham Athletic.
City's head of elite development Patrick Vieira hopes that the teenager can gain some valuable experience with the Scottish Premiership side.
"This is an exciting development opportunity for Ellis. The experience of playing in the Scottish Premiership will be of huge benefit to him," he told the club's official website.
"I'm looking forward to seeing the progress he makes up in Scotland and we wish Ellis and St Mirren well for the coming season."
St Mirren start the new Scottish Premiership campaign away to Motherwell on August 9.