Wagner joins the Division 1 club following one season with VFL side Port Melbourne, where he played nine matches in this year's cancelled season.
The 24-year-old joined the Kangaroos via the 2015 National Draft and made his AFL debut with the Arden Street club the following year.
Wagner was delisted by North Melbourne at the end of 2017 and was recruited to the Demons in 2019 via the Supplementary Selection Period after a season with Casey in the VFL.
The Aspley product was cut from Melbourne after one season and 11 appearances.
Now, Wagner will join the Eagles for next year, with Waite having been announced as a high-profile signing for the NFNL club last month.
Wagner played a total of 19 games across his stints with the Kangaroos and Demons, and was rated among Port Melbourne's best in seven of his nine appearances this year.
Like the VFL season, the NFNL's 2021 campaign was brought to an abrupt ending due to the COVID-19 pandemic, with Whittlesea managing two wins from their 12 matches.
Wagner and Waite will partner against former teammate and North Melbourne great Brent Harvey went the Eagles clash with North Heidelberg next season.