Otis Khan and Tom James were introduced at half-time with the former delivering for the latter to nod home an equaliser on 61 minutes.
AFC Bournemouth loanee Sam Surridge came off the bench to score a fine volley in the closing stages and secure the Glovers top spot in Group, setting up a home tie with AFC Wimbledon in the second round.
“Tactically the substitutions worked really well and we’re pleased to be through,” Way told iFollow Glovers.
“The way the players responded in the second half to a disappointing goal and the impact the substitutes made was very effective against a Plymouth side who were almost full strength.
“I thought we were getting space when we were switching the play and I know Tom James’ quality; he used the width really well and he took his goal well.
“I had a conversation with Rhys Browne against Notts County on the particular role I wanted him to play from the bench; Sam Surridge has gone and done that for us (v Plymouth), Tom James has gone and done it and all the players are developing.
“It took special character and personality to get that game back and that created a special team performance.
“I’ve got a headache going into the weekend but it’s a great one to have.”