Luis Suarez snubbed Patrice Evra’s pre-match handshake ahead of United’s 2-1 win over Liverpool at Old Trafford on Saturday.
Rooney told BBC Sport: "I haven't seen it, obviously a few of the lads were talking about it, but we just had to focus on the game today.
"That's between the two of them and nothing to do with us, let them sort it out. We had to just focus 100 per cent on the game and make sure we got three points and thankfully we did that."
Rooney did, however, make a passing judgement about Suarez's refusal, insisting that if the FA want players to do something then they should, while he would not be bothered if pre-match handshakes were abandoned altogether.
When asked if he would mind if the rule was taken away, he replied: "It doesn't bother me.
"If the FA and the Premier League want us to shake hands then I think that's what we should do.
"But if it's there or not it doesn't bother me. I think it obviously shows the fair play and sportsmanship but you can always do that at the end of the game, but either way it's not really of much concern to me."
The 26-year-old bagged a brace in the first five minutes of the second half and he was delighted with his goals in a deserved victory at Old Trafford.
He said: "The first one I just had a little bit of movement which was key to the half a yard I needed and for the second one Antonio played a great pass to me and I've finished it off."
Suarez grabbed a goal with 10 minutes remaining, which set up a nail-biting finish to the match, but the Red Devils forward thought the team handled the pressure well.
He added: "They got the goal and the last five or 10 minutes they put a few long balls into the box and we had to deal with them.
"I thought we coped with it well and we deserved the three points, although the last five minutes were a bit nervy."
On the field the game was played fairly compared to previous meetings, and Rooney applauded both sets of supporters for their part.
He said: "I don't think there were many bad tackles and not many bookings. I think the game was played quite fairly.
"With everything surrounding the game and what happened the game was played in good spirit, I think both sets of fans did well."
After the game Evra appeared to celebrate in front of Suarez, and Rooney wanted to leave the players involved to sort that incident out.
He added: "These things happen, the same with people talking about Patrice shouldn't have done this, or Luis Suarez shouldn't have done that.
"It's not for us to comment on. It's for them to sort out and we just have to concentrate on the job we had to do today."
The win leaves United top of the table, with Manchester City facing Aston Villa on Sunday.
"[There's] still a long way to go, as I've said before there are many twists and turns to go," Rooney said.
"We're glad we're there, it's nice to be there. We have to keep playing our games and keep winning and hopefully we're top by the end of the season."
The former Everton forward believed both United and Toffees fans will be as thrilled as he is with the win.
He added: “It's always great to score against Liverpool and I'm sure Evertonians will be celebrating tonight.”
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