Giggs was substituted in the second half at the Reebok Stadium and will now miss United's Champions League fixture against Valencia on Wednesday and the Premier League fixture against Sunderland next weekend.
However, striker Wayne Rooney should be fit to play at the Mestalla despite also being substituted after 61 minutes and requiring ice to treat a knock.
"Ryan is the most serious, it's a hamstring and I'm afraid he will be out for a couple of weeks," Ferguson told ESPN. "I'm sure Wayne will get ready for Wednesday.
"In the first half we should have done better but we did well to come from behind. The second half was very even. Bolton were a real handful and our chances were reduced but we must take credit for coming back again, it shows a bit of character.
"I think a lot of teams coming here will find it very difficult. I thought it was a fair result. Teams drop points when we don't expect them.
"Away from home we've scored seven goals and only got three points, it's a very difficult league."
Owen, who appeared as a substitute and scored his 200th club goal with his first touch of the game, was disappointed by United's inability to take full advantage of defeats to Arsenal and Chelsea on Saturday.
"It's always a tough place to come but we created enough chances and dominated most of the game but we're disappointed to only get a point," Owen said. "With the results this weekend it was an opportunity to close that gap at the top but it wasn't to be and we have to focus on our next game now.
"We were helped with a few nice results yesterday but when you don't capitalise fully it's disappointing. It's a long season and we'll bounce back."
Though Owen Coyle admitted to feeling some regret that his side were unable to take all three points, he was delighted with the performance that put Bolton in 12th place with seven points from six games.
"I felt having led twice we had opportunities to see the game through, but there were many pleasing aspects today, we looked fresh and energetic," Coyle said.
"I thought the performance was outstanding. There is a tinge of disappointment but I'm very pleased with how the lads went about it. You have to start well against teams of the calibre of Manchester United and we did that."