The 'Star Trek' actor and the 'Glee' star are said to have parted ways after struggling to make time for each other due to their busy filming schedules.
A source told UsMagazine.com: ''Zach being away and filming was not easy on them. Now he's going to be in New York with his new play ['The Glass Menagerie']. They really loved each other, so it wasn't an easy split.''
There are no hard feelings between the pair and they have apparently remained friends.
The insider added: ''It just ran its course. Zach has been out and about and he seems fine.''
Zachary, 36, and Jonathan, 28, went public with their romance in September 2012, just one year after 'Heroes' star Zachary came out as gay.
He confessed at the time that he hadn't been in a healthy relationship with anyone until meeting Broadway star Jonathan.
He said: ''I'm incredibly happy, I'm incredibly lucky. [In the past] I found myself in a pattern of being attracted to people who were somehow unavailable, and what I realised was that I was protecting myself because I equated the idea of connection and love with trauma and death.''
Meanwhile, Jonathan - who played Jesse St. James on 'Glee', the scheming male lead of a rival glee club - has flown out to console his good friend Lea Michele after the tragic passing of her boyfriend and his former co-star, Cory Monteith.
A source added: ''He flew to be with her as soon as he heard. His heart is broken for her.''
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