While his team-mates were in Saudi Arabia for the Magpies' training camp in Jeddah, Wood was on international duty in Abu Dhabi in the United Arab Emirates.
His 30th-minute penalty cancelled out Ali Olwan's opener and was his 28th international goal, taking him to within one of tying Vaughan Coveny's all-time record.
However, Musa Al-Taamari scored from the spot three minutes later before Olwan netted again to give Jordan the victory.
Wood played the full match, and is likely to be in action again on Tuesday when New Zealand face Uzbekistan in Dubai in another friendly.
The double-header is part of the All Whites' preparations for the Oceania World Cup qualifying tournament, which takes place in Qatar in March.