The bronze went to Jessica Taylor of England.
Theisen-Eaton scored 6,597 points by winning five of the seven events (high jump, shot put, 200m, long jump and the closing 800m), finishing second in the 100m hurdles and placing third in the javelin.
Zelinka (6,270) won the latter two disciplines as she added a matching silver to the one she got at the 2010 Games in Delhi, India.
Theisen-Eaton, a 25-year-old from Humboldt, Sask., was the silver medallist at last year's world championships. This season she broke Zelinka's Canadian heptathlon record at the prestigious IAAF Hypo Meeting in Austria, where she scored 6,641 points.
Theisen-Eaton is married to American Ashton Eaton, the reigning Olympic and world champion in the decathlon and the world record holder.
Her victory Wednesday completed a sweep for Canada in the multi-sport track and field events in Glasgow. Damian Warner won the decathlon a day earlier.
Just before Theisen-Eaton wrapped up her gold, fellow Canadian Derek Drouin won the men's high jump title.
Canada also got gold medals on Day 7 from wrestlers David Tremblay, Arjun Gill and Dori Yeats, and divers Meaghan Benfeito and Roseline Filion in the 10m synchro event.