Natasha Flint's goal separated the sides at half-time but a Rachel Rowe double, both in stoppage time, saw the home side claim all three points.
Lydia Bedford opted to make nine changes from the side beaten by Liverpool in the Continental Tyres League Cup four days earlier, with only Sam Tierney and Flint keeping their places in the starting XI.
The hosts started on the front foot but it was Leicester who had the ball in the net first, though Ashleigh Plumptre fired the ball past Jacqueline Burns after the referee's whistle had gone for a foul in the box.
Reading continued to threaten and from Faye Bryson's cross, Lily Woodham sent a header narrowly wide of the post. Justine Vanhaevermaet was next to take aim, trying to curl an effort into the top corner, but seeing it drop just off target.
There were soon penalty appeals at the other end when Shannon O'Brien struck for goal from just inside the area and appealed that it came off Diane Caldwell's arm, but the referee was unmoved.
Those saves would prove crucial as the Foxes took the lead soon after. O'Brien won possession in her own half, driving forward with speed before an inch-perfect pass to Flint, who took a touch before arrowing the ball into the bottom corner.
Into the second half, Lily Woodham struck over as Reading tried to initiate a response, while there was a chance for Flint to double her advantage when striking from a tight angle in the box, but could only find the side netting.
That would be her last involvement, as Missy Goodwin came on just after the hour mark. More City chances followed, with Aileen Whelan heading wide from Jemma Purfield's cross, before O'Brien nodded Plumptre's centre off target, and was soon replaced by youngster Ava Baker.
It remained at 1-0, giving Kelly Chambers' side hope of a comeback and Rowe came close to providing it, firing wide before Sam Tierney did well to block Emma Mukandi's long-range effort.
The Royals' skipper was in the action again when her cross was headed wide by Charlie Wellings, shortly before Lily Woodham's free-kick had to be punched away by Levell.
Back at the other end, Whelan had two opportunities in quick succession from a Purfield free-kick, seeing a volley blocked, ahead of her second attempt being held by Burns.
Heartbreak was to follow as Rowe's in-swinging corner from the right found its way into the net without a touch on the 90-minute mark.
Six minutes of added time were then signalled, but Rowe needed just 120 more seconds to net her second and the winner, hitting an unstoppable long-range strike into the bottom corner.
Floored by the disappointment, Leicester had little time to find an equaliser and once Goodwin's left-footed effort sailed just over the crossbar, the points were staying in Berkshire.
A cruel ending for City.
A last-gasp Rachel Rowe brace saw the Royals snatch their first success of the campaign in stunning fashion, scoring directly from a corner, before firing in from 25 yards out, just two minutes later.
Natasha Flint's first goal of the campaign - and the first scored by a Leicester player in the WSL this season - looked to have propelled City to their maiden victory of 2022/23.
City's No.7 had opened the scoring at Select Car Leasing Stadium.
Shannon O'Brien and Natasha Flint linked up to great effect in the first half, providing a clear attacking threat to the Reading defence, but the goal they created wasn't enough to take anything out of the game.
Where do we stand?
The Wales international started in a central midfield role for the Foxes.
LCFC Women sit bottom of the Barclays Women's Super League, without a point from the opening six matches.
Leicester were agonisingly close to their first points of the season.
Arsenal are next up for the Foxes in the Barclays Women's Super League, facing the Gunners in a 2pm GMT kick-off at King Power Stadium on Sunday.
City: Levell; Simon, Howard, Tierney, Plumptre, Purfield; Pike, C. Jones (Bott 88'), Whelan (c); Flint (Goodwin 62'), O'Brien (Baker 80').
Subs not used: Lambourne, Poor, Vance, McManus, E. Jones, Scofield.
Goal: Flint 36'.
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