Leading 1-0 from the first leg in Karshi, Nasaf fell behind early in the game at King Abdullah International Stadium when Abdullah Deeb fired in a free-kick for Al Wehdat to level the semi-final tie.
Boskovic, though, headed home the equaliser in the 63rd minute to set up a meeting with Kuwait SC in the final later this month.
"I'm happy with the achievement of the goal in the match, which was to put a great deal of pressure on the Al Wehdat players, and it gave us the chance to control the middle area and control the game," said Nasaf boss Anatoliy Demianenko.
"Al Wehdat are a good team, their chance to qualify to the next round was about 50% after the first match.
"They possess a large number of Jordan national team players, which will be beneficial for them in World Cup qualifying games."
Al Wehdat assistant manager Mihtaz Mendo admitted nerves played their part in the Jordanians downfall.
"Everyone was optimistic before the match and focused on delivering the best performance. However this was not realised on the field. Both teams did not play that well but the nervousness was evident in our players more," he said.
"We were surprised by the lack of a reaction from our players after the goal, we expected a reaction, but several of the players simply became depressed despite them being experienced players."
In Kuwait, Arbil twice came from a goal down to draw 3-3 with Kuwait SC but the hosts went through 5-3 on aggregate.
Kuwait built on their two-goal advantage from the first leg when Boris Kabi gave them an early lead but Arbil hit back through Mahdi Kareem's penalty before Luay Salah fired them into the lead with just over 20 minutes to go.
Rogerio levelled shortly afterwards with a fierce strike and Khaled Al Shammari headed Kuwait SC into the lead before Kareem's second penalty of the evening ensured the game finished all square.
"My happiness is indescribable, I would like to thank the players for their manly performance in the match. They were men in the true sense of the word and gave a big match," said Kuwait SC boss Dragan Talajic.
Arbil coach Ayoub Odisho felt the Iraqis deserved more from the encounter.
"Believe me, we played a very good match and we deserved to at least get the victory," he said.
"Anyway the team that qualified to the final match is not a strange team. It is an Arabic team and a Kuwaiti brother and we wish them luck in the final."