As the nominated nation to qualify on Team GB's behalf, the Lionesses knew they needed to win the match in order to have any chance of competing at the Paris Games next summer.
England need to win their Women's Nations League group and reach the final - or come third if hosts France make the final - in order to qualify.
England went two goals down inside the first 35 minutes on a cold and dreary night at Wembley, stunning the home crowd.
Lineth Beerensteyn twice took advantage of defensive errors and sluggish play to put the visitors in command before half-time against Sarina Weigman's side.
But a stunning second-half turnaround would ensue, first through Georgia Stanway and Lauren Hemp, both of whom scored in a two-minute blitz in the second half.
With the fans re-energised, the Lionesses began to turn on the style as they pushed hard for a winner, ultimately finding the winning goal through substitute Toone, who latched on to a Lauren James pass to score the third in added time.
The match-winner was unsurprisingly delighted with the team's second-half display, telling ITV: "It is always nice to get on the scoresheet. The main thing was to win and we did that. I knew my role was to come on and change the game in any way that I could.
"What a ball from LJ. We showed a lot of character to get the win.
"I thought we played really well. Even at two goals down we dominated the game, and it was two errors from us.
"The character was huge from us, and it was nice to get the win.
"The game against Scotland will be massive. But every game we play is big because everyone wants to beat England, we've got a target on our backs. We'll go there with a game plan and wanting to get the win."
England will reach the Nations League finals with a win over Scotland in their final match on Tuesday night, provided the Netherlands don't win their match against rivals Belgium.
