Layton Ndukwu’s 25th minute penalty cancelled out Lorenzo Gonzalez’s opener for the hosts before Benjamin Garre restored the lead for Simon Davies’ men in Manchester.
When home goalkeeper Arijanet Muric spilled substitute Josh Eppiah’s low drive with seven minutes remaining, however, Thomas was perfectly positioned to find the bottom corner.
It is a result which nudges the Foxes up to fifth in the fledging Division 1 standings ahead of the Checkatrade Trophy trip to face Fleetwood Town at Highbury Stadum on Tuesday evening.
Despite a decent start, City fell behind in just the 10th minute when Garre spotted Gonzalez in space behind the backline and the Swiss-Spanish dual national slotted it in.
The hosts, who had İlkay Gündoğan among their ranks, almost doubled their advantage when Brahim Diaz cut inside Connor Wood and sent his low shot toward the base of Eldin Jakupović’s post.
Beaglehole’s Foxes levelled the scores before the half-hour when Ndukwu stepped up assuredly to convert from 12 yards after Thomas had been felled in the box.
Leicester grew into the match as the clock ticked down in the first half, moving the ball around confidently and looking dangerous through wide men Admiral Muskwe and Ndukwu.
After the break, though, it was Davies’ hosts who regained the advantage when Phil Foden located Garre in space at the far post to place it beyond Jakupović.
With 10 minutes left, excellent play from the Foxes almost opened Man City up as Khanya Leshabela gave it to Eppiah, who found Liandro Martis, but the Curacao international’s cross was cleared.
Martis was having an impact on the match. When his cross fell to Eppiah in the box, the 18-year-old’s shot seemed destined to ripple in Muric’s net.
The shot-stopper got a hand to it but didn’t legislate for Thomas as the Foxes new boy squeezed it beyond his grasp to secure a crucial point for Beaglehole’s men.
Key moment
It was the goal which ultimately rescued a point for the battling Foxes in Manchester.
After his introduction in the 71st minute, Martis was a menace and his cross lead to City’s second, finding Eppiah, whose shot fell right to Thomas to finish well.
Who impressed?
Beaglehole needed an extra spark on the pitch as his side went in hunt of an equaliser in the latter stages and, when he looked to the bench, he found Martis ready to come on.
The 21-year-old's arrival proved to be the turning point for City as they hurried their hosts down and eventually got their reward with Thomas’ timely strike.
Midfielders Kaba Sherif and Hamza Choudhury also deserve a mention for professionally handling German international Gündoğan for an hour.
Coming up…
City travel to Highbury Stadium for their opening Checkatrade Trophy group stage clash of the season against Fleetwood Town on Tuesday evening (7:45pm kick-off).
After a break from action, Beaglehole’s men then welcome West Ham United to King Power Stadium on Monday 11 September (7pm kick-off), which you can watch live on LCFC TV.
Man City: Muric, Duhaney, Oliver, Francis, Davenport (c), Smith, Diaz, Gündoğan (Latibeaudiere 61 (Ogbeta 90)), Gonzalez, Foden, Garre.
Subs not used: Haug, Dele-Bashiru, Richards.
Goals: Gonzalez 10, Garre 50.
City: Jakupović, Pascanu, Wood, Choudhury (c), Knight, Johnson, Ndukwu, Kaba Sherif (Leshabela 71), Gordon (Martis 71), Thomas, Muskwe (Eppiah 65).
Subs not used: Debayo, Iversen.
Goals: Ndukwu (pen) 25, Thomas 83.
Referee: Marc Edwards
Attendance: 568
Images: MCFC/Getty