The Argentine striker made his second West Ham appearance off the bench against Phoenix but was unable to stave off defeat in the club's opening game on their New Zealand tour.
In a sluggish first half, the Premier League side conceded early on to an Andrew Durante header as their underwhelming pre-season form continued.
Sam Allardyce saw his men draw against Stevenage and Ipswich Town and things got worse when Alex Gorrin doubled Wellington's lead with a long-range strike.
Former Lazio man Zarate struck 19 minutes from time to halve the deficit, yet it mattered little as the A-League side saw out the victory.
Allardyce's men made a slow start to the fixture and were punished after just 12 minutes, their defence caught napping as Gorrin crossed for Durante to head home.
It was all too easy for Wellington, who doubled their lead through Gorrin soon after - the former Sunderland man firing past Jussi Jaaskelainen from the edge of the area.
With West Ham trailing by two goals at the break, Allardyce brought on recent signings Zarate, Diego Poyet and Cheikhou Kouyate for a taste of the action.
Zarate was on target within 11 minutes of entering the fray, as his long-range strike found its way past Glen Moss after Stewart Downing had jinked in from the left wing.
Despite late pressure, which saw Zarate flick an effort narrowly wide of the post, Allardyce's side were left to lament a slow start ahead of Saturday's clash with Sydney.
