Thomas’ late run in at the back post was not tracked and, when the ball fell at his feet following a low cross from the City right, the Foxes captain could make no mistake from close range.
The visitors also had two goals chalked off in the first half for offside, but that belies the Young Blues’ efforts on the night, who continued to pile on the pressure despite falling behind.
But it was to no avail, as George Hirst stroked home in stoppage time to extend City’s winless run in Premier League 2 to six matches.
City zipped the ball about confidently in the early stages, but it was the visitors who had the first real sight of goal when Calvin Ughelumba got on the end of a deep free kick with six minutes on the clock.
However, he failed to make enough contact, and his glancing header sailed harmlessly wide of Daniel Grimshaw’s net.
Undeterred by that early chance, Paul Harsley’s men continued to enjoy large portions of possession in the Leicester half and, after an Iker Pozo through ball, Morgan Rogers could have found himself in on goal after ten minutes but for the offside flag.
That spell of pressure seemed to bring the visitors to life, and two quick chances followed with the 20-minute mark approaching.
Callum Wright was threaded through on the right-hand-side of the City box, but he was crowded out by a combination of the onrushing Grimshaw and Tyreke Wilson and failed to hit the target.
Moments later, Grimshaw had to once again be on hand to parry a long-range, dipping Admiral Muskwe strike out for a corner.
The Foxes were then even closer to breaking the deadlock, when they had the ball in the net in the 28th minute, but referee Benjamin Speedie ruled out a towering header for a foul in the build-up.
The heavens had opened at the Academy Stadium, but the Young Blues were weathering the Leicester storm.
And it was not all one-way traffic with City still pressing for the opener, and they almost had it when Tommy Doyle raced through the middle and looked to play in Ben Knight.
However, our skipper put a little bit too much weight on his pass, and the danger was smothered by Johansen.
Leicester had the ball in the net once again with half-time approaching through Wright, but his volleyed effort was once again ruled out for offside after the ball rebounded back to the winger off Muskwe, who had strayed past City’s defensive line.
Into the second half and substitute Josh Eppiah should probably have opened the scoring for the visitors when sent through within minutes of the restart, but Grimshaw was off his line in a flash to smother the danger.
With an hour of the game gone City once again began to find their feet, and good work from Rogers down the left saw the ball reach captain Doyle on the bounce.
The midfielder’s drilled half-volley on the edge of the box looked destined for the top corner, but Johansen pulled off an excellent save to tip the effort over the bar.
The Young Blues’ continued to pile on the pressure, and claimed for a penalty when Alpha Diounkou felt he was pushed in the box as he rose highest from a corner.
But his and his teammates’ claims for a penalty fell on deaf ears.
The game’s only goal arrived in the 77th minute when a low cross into the City box was half-cleared to the back post, where the onrushing George Thomas took a touch and smashed into the net.
The Young Blues were visibly disappointed to concede after competing throughout the second half, and 16-year-old Liam Delap came on in the aftermath of the goal to add some spark to Paul Harsley’s side.
We continued to push for an equaliser, Diounkou going close with a header from a stoppage-time corner.
Unfortunately, that pressure on the visiting goal left gaps at the back and, after a swift counter down the left wing, Foxes striker George Hirst cut in on his right foot and calmly dispatched his fifth league goal this season to seal the points.
How we lined up
Daniel Grimshaw started between the sticks, protected by a back four of Alpha Diounkou, Rowan McDonald, Taylor Harwood-Bellis and Tyreke Wilson
Iker Pozo sat in front of the defence, with Fisayo Dele-Bashiru and Tommy Doyle his midfield partners.
Finally, at the sharp end of the team, Adrian Bernabe and Morgan Rogers provided width for centre-forward Ben Knight.
What it means
The defeat means City remain in 12th place in Premier League 2, four points adrift of safety.
City Under 19s travel to Italy to take on Atalanta in a crucial UEFA Youth League clash on Wednesday 6 November with the game scheduled to kick off at 13:00 GMT. The Young Blues’ next Premier League 2 match is away to Blackburn Rovers on Friday 22 November.