"It's a feature that's been gone for 50 years, so it's good to have it back," master stonemason Marcus Wainwright said.
The window had to be pinned to the stone on one side and set with lime mortar on the other, to guard against future shifting.
"All the structural keys were done with cement, originally. But with old buildings like this, they will move. When lime mortar gets fractures it heals itself, to an extent. The crystals rebond," he said.
Mr Wainwright has spent most of this year carving three Oamaru stone crosses, four finials and three tracery windows for the tomb.
"It's unique in the southern hemisphere and it's not the sort of thing we get to work on every day," Dunedin Monumental Masons stonemason Craig Morton said.
Mr Wainwright was one of the few people in New Zealand who could do the work, he said.
The restoration will include installation of a sophisticated new camera security system.
The mausoleum, designed by celebrated Dunedin architect R. A. Lawson in 1881, reflects his design for First Church, in Dunedin.
It houses the remains of Dunedin businessman and MP William Larnach (1833-98), his first two wives, Eliza and Mary, his eldest daughter Kate and eldest son Donald.
The Historic Cemeteries Conservation Trust of New Zealand raised $345,000 for the restoration.
"We hope to have all the stained glasswork in by July next year," chairman Stewart Harvey said.
Dunedin stained glass artist Peter Mackenzie has imported antique stained glass from France to complete the restoration.
