The 45-year-old stepped up from the club's Under-23 team in October after Robin Dutt had been sacked following a dismal start to the season.
Under Dutt, Werder failed to win a single league match and were bottom of the table when Skripnik took over.
His arrival sparked an immediate upturn in form as Werder claimed three successive wins in all competitions, only tasting defeat for the first time last weekend against Hamburg.
Following his impressive start the club have tied him, and his coaching staff, down to a new deal that will see Skripnik remain at Werder until June 2017.
"We are delighted that this trust is placed in us," said Skripnik. "We are connected by a major identification with the club.
"We will do everything we can to be successful again.
"We want to get out of the relegation battle as quickly as possible and continue to develop the team."
Werder could be out of the bottom two this weekend if they can beat Paderborn and other results go their way.
