In a see-sawing affair on Friday night at AAMI Park, the Rebels scored five tries to three with Gordon picking up one himself en route to a 34-27 victory.
The Waratahs were coming off a rallying win over Fijian Drua in round two but were out-enthused by a desperate home side, who have now won three straight against NSW in Melbourne.
The visitors had to scramble after three key men were late withdrawals, losing hooker Dave Porecki (infection), winger Max Jorgensen (shoulder) and flanker/lock Ned Hanigan (knee).
The Tahs started strongly but had two tries denied within two minutes with winger Nemani Nadolo edging the sideline as he planted the ball before No.8 Langi Gleeson was ruled to have propelled himself over the line after being tackled.
Feeling luck was on their side, the Rebels rose to the occasion and scored the next three tries.
Centre Reece Hodge crossed off a Lachie Anderson kick into the in-goal and then three minutes later they swapped roles with the fullback managing to ground a Hodge kick as he dived over the sideline.
Melbourne No.8 Richard Hardwick, who has been a stand-out this season, continued his try-scoring spree for the Rebels to go in at halftime up 17-6, with Hodge missing two conversions.
However the Waratahs regrouped at the break and regained the lead 20-17 when Charlie Gamble scored their second try of the half.
With 22-year-old Gordon's passing first-rate and kicking game en pointe, the Rebels refused to lay down and were back in front with prop Matt Gibbon out-smarting the defence in the 60th minute.
Gordon's try under the posts four minutes later gave the home side some breathing space.
NSW at least scored a converted try in the 80th minute through lock Taleni Seu to snatch a losing bonus point.
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