The visitors took the field without David Villa, the NYCFC talisman -- just two goals shy of 400 in his career for club and country -- a late scratch after feeling something in warmups. He was replaced byJo Inge Berget in Patrick Vieira's lineup.
San Jose was up in the third minute after Yefferson Quintero.headed a Magnus Eriksson corner into the NYCFC goal from the near post to make it 1-0.
NYCFC then took the lead on the hour mark, afterAnton Tinnerholm smashed a first-time half-volley pastAndrew Tarbell and Maxi Moralez scored from aIsmael Tajouri assist courtesy of a wicked deflection to make it 2-1 in the visitors' favor.
Johnson played a big part in preserving his team's three points as the game wore on, repeatedly turning quality Quakes chances away in the last 20 minutes.
And Vieira's team held on through a full seven minutes of stoppage time to take home a valuable win in this young MLS season.
San Jose 1-2 New York City FC: NYCFC stay unbeaten
David Villa's absence didn't stop NYCFC from overcoming an early deficit to beat San Jose and remain unbeaten to start the season.
WATCH: Tinnerholm's volley brings NYCFC level
Major League Soccer: Anton Tinnerholm (49') San Jose Earthquakes 1-1 New York City FC