How does Eddard Stark know that Bran saw Cersei and Jaime together?

He made an educated guess, based on the information he had.

At this point in time, Ned knows or has worked out that:

• Cersei and Jaime are secretly lovers;
• Bran fell, despite being an excellent climber, on a day when Cersei and Jaime were left in Winterfell while nearly everyone else was out hunting;
• someone, probably a Lannister (he's got the wrong one, but never mind) sent a man to kill Bran.

Clearly somebody wants Bran dead. Why? A child can't pose any threat to the Lannisters or anyone else, except by the information inside his head. What could he know that would be dangerous to the Lannisters? Presumably the same dark secret that got Jon Arryn killed. How could he have found it out? It's a reasonable guess to say he found out on the day he had his near-fatal accident, and found out in the simplest way possible - by seeing Jaime and Cersei together as lovers rather than siblings.

In the book A Game of Thrones, where of course we see a lot more of Ned's internal monologue, his musings with regard to Bran are made more explicit:

• Lord Stannis shared the secret Jon Arryn had died for, he was certain of it. The truth he sought might very well be waiting for him on the ancient island fortress of House Targaryen.

  And when you have it, what then? Some secrets are safer kept hidden. Some secrets are too dangerous to share, even with those you love and trust. Ned slid the dagger that Catelyn had brought him out of the sheath on his belt. The Imp's knife. Why would the dwarf want Bran dead? To silence him, surely. Another secret, or only a different strand of the same web?

  _{-- A Game of Thrones, chapter "Eddard VIII"}

• And yet, he knew he could not keep silent. He had a duty to Robert, to the realm, to the shade of Jon Arryn … and to Bran, who surely must have stumbled on some part of the truth. Why else would they have tried to slay him?

  _{-- A Game of Thrones, chapter "Eddard XII"}

Although in the book, this part of Ned's conversation with Cersei plays out slightly differently. Instead of stating his suspicions about Bran outright, Ned lets Cersei confirm them:

"My son Bran …"

To her credit, Cersei did not look away. "He saw us. You love your children, do you not?"

_{-- A Game of Thrones, chapter "Eddard XII"}

There was some good guesswork going on, and it was also probably a test.

Several points to consider.

1. By now Ned Stark has found compelling evidence that one of his best friends (the king) is being cuckolded. At some level, he starts to actively dislike Cersei because of this. Ned has actively disliked Jamie since he became a Kingslayer.

2. Cersei and Jamie are together at Winterfell, doing what it is they do. If they were intimate there, they would have had to keep it secret at all costs.

3. Bran climbs like a stealth monkey. No one notices the breathtaking feats he achieves until he is occasionally spotted. When he is not spotted, he is uninjured to the point of showing not even a scratch.

4. Bran doesn't fall.

5. Against Jamie's potential avarice (and Cersei's heartlessness), Bran has no defense.

6. Jamie and Cersei had the need to be alone in secret. Bran is a stealth monkey. If "a problem" arose, Jamie and Cersei had the motivation, opportunity, and disposition to murder the son of their host.

It would not be a surprise that Ned strongly suspected Cersei. What might be surprising is that he mentioned it to her straight up. He may have wanted confirmation by seeing her reaction to the statement. He got it.

Don't know why no one is mentioning this, but Eddard's wife found a blond lady's strand of hair when she was looking around the tower from which her son fell (actually was pushed). That kind of hair (length and color) wasn't too common that side of the kingdom(s), and at a watch tower of all places. This already meant the place was likely used as some kind of sexual rendezvous. The wife must have told Eddard this, remember she meet Eddard at the brothel later on. To me this was the greatest hint then added to all that mentioned in the other answers confirmed to Eddard what must have made his son fall.