The 32-year-old Socceroo, who first joined the Hibees more than a decade ago, helped the Edinburgh club capitalise on a 34th-minute dismissal for Vukasin Durdevic as they pulled off one of their most notable European results in decades in the Serbian capital.
Captain Boyle scored his 100th goal for the Hibees in the 40th minute before notching his second of the evening from the penalty spot midway through the second half as Gray's side seized full command of their Conference League third qualifying round tie at the half-way stage.
"Martin Boyle constantly delivers for this club," Hibs boss Gray told BBC Scotland.
"That's 101 goals now, to do that shows how much of a threat he is and he demonstrated that again tonight.
"Not just that, I spoke a lot last season about him and the leadership skills, he needed that extra responsibility to take him on to the next level and he's delivering.
"I'm delighted for him on a personal note because he's been sitting on 99 goals for a while now, so he can start passing to other players now!"
If Hibs can close out the tie in the return leg at Easter Road next Thursday, they will face a Conference League play-off against the loser of the Europa League qualifier between AEK Larnaca and Legia Warsaw, with the Cypriot side leading 4-1 after the first leg.
Gray was thrilled with the result in the hostile Partizan Stadium on a special night when the club turned 150.
But he is not taking anything for granted.
"To come here and win 2-0 was unbelievable," he said. "It was some effort. You ask the players to come over here and make sure the tie is still alive when you go home, and we've certainly done that.
"We've put ourselves in a fantastic position but I reminded the players it's only half-time in the tie. Based on our second-half performance, there's plenty to improve on."
In some of the other Conference league action, Tammy Abraham scored a first-half hat-trick as Besiktas completed a comfortable 4-1 win over St Patrick's Athletic at the Tallaght Stadium.
Joao Mario put the Turkish side ahead before former Chelsea forward Abraham, who joined in the summer from Roma after spending last season on loan at AC Milan, tapped in from close range on 14 minutes.
Abraham, capped 11 times by England, doubled his tally with a neat finish before adding a penalty just before half-time.
Dundee Utd also gave themselves a good chance of further progress after battling to a 2-2 draw at Rapid Vienna.
Rapid saw a late goal from Louis Schaub ruled out for offside in the build-up to leave the tie delicately poised.
In some of the Europa League first-leg of third-round qualifying, Panathinakos drew 0-0 with Shakhtar Donetsk at home with PAOK playing to the same scoreline, also at home, to Wolfsberg.
Midtjylland beat Fredrikstad 3-1 while Braga were also successful away, winning 2-1 at Cluj.
