Referee Chris Foy awarded United a 19th-minute penalty after Ronaldo had gone down under keeper Mark Schwarzer's challenge, although replays suggested the anger of the home fans was justified.
Louis Saha exorcised the ghost of his Champions League miss against Celtic by sliding home the spot-kick, but United were pegged back on 66 minutes when substitute James Morrison equalised.
• Southgate accuses Ronaldo of cheating
However, United needed less than two minutes to restore their advantage, Darren Fletcher heading home the winner.
That United deserved to lead at half-time was not in any doubt, but the way in which they achieved it left a sour taste in the mouths of the home fans.
Saha turned just inside the Boro half to race past Jonathan Woodgate and slide a pass to the unmarked Ronaldo. He took the ball in his stride and cut inside Schwarzer, plummeting to the ground in the process.
Foy pointed immediately to the spot, but what contact there was, if any, was minimal. However, Saha stroked the spot-kick past Schwarzer to make it 1-0.
Boro might have been level within two minutes, but Abel Xavier hit a post with a header from Stewart Downing's free-kick in his first home game since his drugs ban expired.
However, Morrison struck on 66 minutes when Downing cleverly evaded Gary Neville's challenge to cross and Gabriel Heinze's weak header fell to the midfielder, who volleyed past Edwin van der Sar to level.
But Boro's joy was short-lived and ended within two minutes as Ryan Giggs picked put Fletcher's run into the box after Ronaldo had left the Boro defence standing and the Scot headed powerfully home.
Southgate accuses Ronaldo of cheating
Middlesbrough boss Gareth Southgate accused Manchester United winger Cristiano Ronaldo of cheating after he earned his side a controversial penalty at the Riverside Stadium.
Television replays showed that Boro goalkeeper Mark Schwarzer made no contact
with the Portuguese international in the 19th-minute incident which saw referee
Chris Foy give Louis Saha the chance to fire his side ahead.
Asked if Schwarzer felt he had been cheated, Southgate replied: 'Yes, it is
as simple as that.
'It is very difficult for the referee because it happens very quickly, but
how many times are we going to see it?
'The lad has got a history of doing it and in the end, that has cost us the
game.
'If you go behind to a goal against a team like United, it is a mountain to
climb.
'Our goalkeeper has done everything he can to get out of the way. There was
clearly no contact, I did not think so at the time and when you see the replays
there is nothing there.
'For me, it is never a penalty.
'I do not know what you do. That is for people who are better qualified than
me to deal with.
'I am not interested in talking about him, really. He plays the way he
obviously thinks is the right way. That's fine, but on the day, that has given
us a mountain to climb.'
Saha's spot-kick was cancelled out by substitute James Morrison's 66th-minute
strike but Darren Fletcher headed home a Ryan Giggs cross two minutes later to
extend United's lead over Chelsea at the top of the Barclays Premiership to six
points.
Asked about the incident, United boss Sir Alex Ferguson said: 'I thought it
was a clear penalty to be honest with you.''
After being shown a replay, he added on PremPlus: 'He is trying to evade it,
isn't he? But would he have scored? I think he would have.
'Anyway, it is a penalty kick.'
Ferguson was delighted with the three points on an evening when his side
perhaps should have killed off the game long before they did.
Ronaldo, who was booed at virtually every touch after the penalty incident,
repeatedly carved the Teessiders open, although they rallied after the break and
might have snatched a point in a late flurry.
The win extended United's unbeaten run in the Premiership to 11 games and made
it eight away games in the league without defeat.
Ferguson said: 'Today was a very important result for us. It is not an easy
place to come to, as we have experienced in the past, but they showed a great
resolution today.
'Even when they equalised they came straight back at them and they wanted to
win it.
'That is important. It is not an easy place and it was a very difficult
game.
'It was hard for the referee with the crowd but it is a good result.'
A clearly angry Southgate was nevertheless happy with the efforts of his
players.
He added: 'It was always a very tough game for us. They are the best side, at
the moment, in the league and it is made a lot harder when you go behind to a
goal like that as well.
'We started the game quite brightly, we were well in it when they scored and
that knocked our confidence a bit, and when you go behind to a team like United,
it is a very difficult ask to come back.'
Middlesbrough 1 - 2 Manchester United
