The Imps ended a momentous 2017 on a winning note thanks to a brace from Matt Rhead, either side of Christian Doidge’s equaliser.
The victory left City third in League Two and saw them close the gap to top two Notts County and Luton Town, who both suffered surprise defeats.
But Cowley, who punched the air with delight at the final whistle, said the result was worth more than three points.
“Sometimes wins go beyond the win, loss or draw column. Some results are more important than that,” said the Imps boss.
“There’s obviously a lot of rivalry between the two teams. I am disappointed with some comments they have made about our players.
“I was disappointed with an incident after the game at their place earlier in the season [Rovers keeper Bradley Collins was accused of spitting at City’s Sean Raggett, although he was cleared of any wrongdoing by the FA].
“I was disappointed with their manager’s comments on the back of us getting promoted. We found them disrespectful, unnecessary and unfounded.
“So it [the game] felt personal, which was fine for us and we enjoyed the win.”
Like in the reverse fixture between the sides in September, the final whistle was followed by a bout of pushing and shoving between both sets of players and coaching teams.
“It was nothing really,” added Cowley. “I was trying to shake their hands but it wasn’t possible.
“There was an incident on the pitch but it was at a pretty low level. You have to do your fighting on the pitch and I thought we did that today.
“I wouldn’t want that incident at the end to gloss over what was a really hardworking and determined performance from us.”
The defeat left Forest Green rooted to the foot of the table although manager Mark Cooper insisted his side deserved something out of the game.
The Rovers boss was aggrieved that his side had a late goal disallowed.
“The referee couldn’t wait to disallow the goal, which always happens here,” said Cooper, who revealed he plans to overhaul his squad during the January transfer window.
“You can’t keep making those horrendous mistakes that lead to goals and expect to win games,” he said.
“We have to keep going and make sure the recruitment in January is spot on.
“We’ve got to make sure we integrate the players coming in and possibly add a couple more on top of that.
“I’ve told the [current] players that I can’t protect them anymore. There’s going to be a lot of new players coming in that are going to give us a boost to make sure we stay in the league.
“These signings will be experienced at this level and know what it takes.”
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