After a goalless first half, Rooney's close range strike on 48 minutes eased the tension that had been gathering over Wembley, especially after news had filtered through of a victory for qualification rivals Ukraine during the half time break.
Branko Boskovic's own goal doubled the home side's advantage 13 minutes later before Dejan Damjanovic dragged Montenegro back into the game and sent nerves jangling once more.
However, a spectacular goal from debutant Andros Townsend and a stoppage time Daniel Sturridge penalty secured the points and means victory over Poland on Tuesday will seal England's place in Brazil next summer.
"It was a tough game," Rooney told Sky Sports. "First half they defended deep and defended well but we still created a few opportunities.
"So we came in at half time knowing we could create chances against Montenegro.
"I think getting the goal so early in the second half was vital and we excelled after that and deserved the three points.
"I think you saw a weight come off everyone's shoulders. It was always going to be a night where we had to be patient and try and break them down but getting that goal was vital for us."
Rooney also praised the bold attacking team selection by boss Hodgson, which saw Rooney form a striking quartet alongside Sturridge, Townsend and Danny Welbeck.
"It was great," he added. "Exciting, with a lot of speed and with experience of Steve [Gerrard] and Frank [Lampard] behind us.
"The manager gave us the freedom and platform to go out and express ourselves and I thought the four of us did that, especially Andros[Townsend], that was some debut."