Woodgate, who was a youth-team player with Boro before spells at Leeds United, Newcastle United, Real Madrid and Tottenham Hotspur, will join head coach Steve Agnew's staff.
Agnew has been in charge since Spaniard Aitor Karanka left the club this month.
"Jonathan is someone who we know very well, and who in turn knows this club inside and out," Agnew told the club website.
"He brings a wealth of experience from the highest level of the game, and he's a fantastic character. We're delighted to have him on board."
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Woodgate, part of the Leeds side to reach the Champions League semi-finals in 2001, ended his playing career last season after helping Boro back to the Premier League in his second spell at the club.
Boro are battling to avoid an immediate return to the Championship having dropped to 19th in the table.
They are without a league victory in their last 11 matches and face a relegation clash with Swansea City on Sunday.
(Reporting by Martyn Herman, editing by Ed Osmond)
