Town's 28-year-old midfielder Jonathan Hogg was carried off with a neck injury, resulting in 14 minutes of stoppage time, after a collision with team mate Mark Hudson.
Hogg, who was conscious and talking in the dressing room, was taken to hospital for precautionary scans.
City then took the lead through Lee Tomlin on the half-hour and Chelsea loanee Tammy Abraham made it 2-0 with his 22nd goal of the season in added time ahead of the break before Aden Flint and a David Cotterill penalty secured the points.
Reading took the lead at Wednesday after 13 minutes through Yann Kermorgant but had keeper Ali Al Habsi to thank for several key saves, including keeping out Jordan Rhodes and Will Buckley.
The home side pushed for an equaliser and sent keeper Keiren Westwood up for a late corner but Reading broke away and Adrian Popa put the ball into an unguarded net to seal the victory.
Reading are five points clear of sixth-placed Wednesday, who occupy the final playoff spot, and a point above Leeds United who next host Brighton while Newcastle visit Birmingham City.
(Writing by Ken Ferris; Editing by Greg Stuchbury)
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