The 23-year-old has made 58 Bundesliga appearances for Bremen since signing in 2011, but only seven starts in their disappointing 2013-2014 campaign.
Ignjovski, who has been linked with a move across Germany to Eintracht Frankfurt, has decided to call time on his Weserstadion stay in the summer to seek more regular football in his preferred position, but has stressed that he will give his all until then to aid their relegation fight.
He told Bild: "I have informed the club that I'll go to the end of the season.
"It was a difficult decision. The aim was not primarily about money. I'm a defensive midfield player and want to prove myself in the future in this position.
"I had a wonderful time here. I assure you that I will give everything to the last second, so Werder remain in the Bundesliga."