"Most of us first met this man when he was dancing in his underwear and feeling the need for speed," Holmes said before introducing a clip reel of Cruise's film history, which she watched with rapt attention. At the end, the actress pumped her arms, then marched off stage to retrieve Cruise who was waiting in the wings, a move that mirrored Cruise's much-replayed performance on the Oprah Winfrey Show last month.
Cruise beamed at Holmes and laughed off the audience's encouragement to "kiss her," saying: "If I've been able to entertain you at all, then, I thank you for allowing me to do so."
Backstage, the couple walked with their arms around each other and Cruise told PEOPLE: "It was an honor" to take home the award.
Cruise's ex-wife, Nicole Kidman, was also on hand at the show to present the breakthrough female award to Mean Girls co-star Rachel McAdams, but Kidman managed to steer clear of her ex, with whom she has two children.
There was one major reunion at the awards ceremony, however. Most of the cast of the hit 1985 movie The Breakfast Club came together for a 20th anniversary tribute to the teen drama. Stars Molly Ringwald, Ally Sheedy, and Anthony Michael Hall received the award – an oversized bucket of silver popcorn.
Regarding being with her co-stars, Ringwald told PEOPLE: "It was really emotional for me – I couldn't believe so much time has passed because we all fell right back into our roles."
Ringwald also told PEOPLE that she is in the early stages of negotiating to do a sequel to her 1984 teen hit Sixteen Candles. "I have a lot of ideas, but nothing I can talk about yet," she said.
The MTV Movie Awards were hosted by former Saturday Night Live star Jimmy Fallon at the Shrine Auditorium. The ceremonies are scheduled be broadcast June 9.