The German international curled home a trademark free-kick in the 64th minute to make it 2-1 after Sky Blues took the initiative with two goals in quick succession at the start of the second half.
But Coventry finished the stronger and the impressive Ben Mackey grabbed a late third goal in the last minute.
It means the reserves have lost just three times in their last 16 FA Premier Reserve League games.
Ziege completed the 90 minutes as did Dean Richards, the big defender putting in a full shift in only his second reserve appearance of his comeback from injury and a virus.
Lee Barnard came closest to opening the scoring when he struck the post in injury time otherwise it was an opening period devoid of clear-cut chances.
We managed to put some decent moves together without finding a cutting edge in the danger areas.
One of those moves completely opened Coventry up as Rohan Ricketts slid in Christian Ziege, he opted to square rather than shoot and his cross somehow dissected the supporting Ricketts, Barnard, Mark Yeates and Gus Poyet.
Ziege earlier headed Danny Foster's cross wide as we looked a threat down the right side with Foster and Marney.
Coventry's only real effort - barring a disallowed goal in the 20th minute, clearly offside - came a minute before the break when Ben Mackey looped a header wide.
As we ticked into injury time Marney got away again down the right, reached the byline and pulled his cross back for Barnard whose side-foot hit the footof the post.
The second half was a different story, ignited by a wonderful opening goal.
With 49 minutes on the clock, Andy Hall's free-kick cannoned back off the defensive wall only for the same player to crash an unstoppable full volley into the top corner from 25 yards.
More action followed in the next 15 minutes than in the first half.
Marney had penalty claims waved away when he was blocked off by Liam Nicell and Poyet's shot from a clever free-kick routine with Ziege deflected into the arms of Richard Brush but within seconds it was 2-0 as Mackey took Craig Reid's pass in his stride, held off Marcel McKie and fired low through Burch's legs and home, 59 minutes now on the clock.
Within a minute of that strike Barnard should have pulled a goal back only to head Marney's pinpoint cross straight at Brush.
But we were soon back in it as a foul on Poyet led to Ziege special on 64 minutes, a delightful curling free-kick from 25 yards into the top right corner.
The game went back into a lull barring a couple of breaks from the lively Mackey but the same player livened procedings up again by first hitting the side-netting and then clinching it for the home side with a fine third goal, holding off Marney before shooting low into the bottom corner in the last minute.
Rohan Ricketts was denied by Brush's fingertip save in injury time - the final action of the reserves' competitive season.
Injury time: WOODWORK. Marney break down the right, pull back from byline side-footed onto post by Barnard.
Half-time: Coventry 0, Spurs 0
49mins: GOAL. Hall free-kick came back off the defensive wall only for same player to volley back unstoppable shot into top corner from 25 yards. 0-1.
59mins: GOAL. Mackey onto Reid pass, held off McKie and shot through Burch's legs from 12 yards. 0-2.
64mins: GOAL. Ziege special, a free-kick from 25 yards curled into the top right corner. 1-2.
89mins: GOAL. Mackey held off Marney before shooting low into far corner. 1-3.
Line-ups: Coventry City: Brush, Whing, Nicell, Barry (Partridge, 65), Briscoe, Osbourne, Hall, Thornton, Reid (O'Donovan, 77), Mackey, Jephcott (Hughes, 85). Subs: Oddy, Belford.
Spurs: Burch, Foster (Daniels, 71), McKie, Richards, Bunjevcevic (Wright, 45), Marney, Poyet, Ricketts, Ziege, Yeates, Barnard. Subs: Eyre, Malcolm.
A Christian Ziege special failed to prevent a disappointing end to what has been a fine second half of the season as our reserves lost 3-1 at Coventry City on Tuesday night.