Charlie Wellings’ drive into the far corner from 14 yards gave Reading the lead halfway through the second half.
Viviane Asseyi equalised when she poked home a stunning curling cross from substitute Izzy Atkinson.
However, Rowe drove into the top corner from 20 yards, despite Mackenzie Arnold getting her fingertips to the shot.
The win sees Reading open up a four-point gap on the league’s only relegation spot which is currently occupied by Leicester, who were beaten by Manchester United earlier on Sunday.
It also sees them climb above Tottenham, Tottenham, who lost at Manchester City, and Brighton, who are not playing this weekend.
Kelly Chambers’ side have played a game more than Leicester and Tottenham and three more than Brighton though so remain in trouble.
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West Ham started the game strongly with Honoka Hayashi, Amalie Threstrup and Lucy Parker all having efforts saved by the impressive Grace Moloney.
Reading grew into the game with Wellings volleying a glorious chance from five yards over the bar at the end of the first half.
The opening exchanges of the second half were scrappy with both sides lacking quality and confidence.
The first goal came after Rowe controlled a cross from the left and laid off for Wellings to fire home her third league goal of the season.
West Ham’s deserved equaliser was a moment of class from Atkinson, her ball cutting out the entire Reading defence to allow Asseyi to score the Hammers’ first league goal of the calendar year.
Rowe’s late curler sparked joy among the Reading players, coaching staff and fans – and it could prove to have been a crucial moment as the season draws to a close over the next three months.