He said the rest of the world had a huge stake in ensuring that a functioning Syria emerged.
"The outcome is Syria is not going to be ideal," he acknowledged, adding strengthening a credible opposition was crucial.
Eager to resolve another source of tension in the region, the President earlier helped broker a phone call between the Israeli and Turkish Prime Ministers that led to the restoration of normal diplomatic relations between the two countries.
Obama had come to Jordan from Israel, where Israeli Prime Minister Benjamin Netanyahu placed a call to Turkey's Recep Tayyip Erdogan to apologise for the deaths of nine Turkish activists in a 2010 Israeli naval raid on a Gaza-bound international flotilla. "The timing was good for that conversation to take place," Obama said.
Obama, at a joint news conference with Abdullah, said his Administration was working with Congress to provide Jordan with an additional US$200 million ($239 million) in aid this year to cope with the massive influx of refugees streaming into the country from Syria.
Abdullah said the refugee population in his country had topped 460,000 and was likely to double by the end of the year, the equivalent of 30 million refugees in the United States, he said.
Obama also said he would "keep on plugging away" in hopes of getting the Israelis and Palestinians to reach a peace agreement. "The window of opportunity still exists, but it's getting more and more difficult," the President said. "The mistrust is building instead of ebbing."
On Iran, Obama reiterated that the US was open to "every option that's available" to keep the country from developing a nuclear weapon. He said it would be "extraordinarily dangerous" for the world if Iran did become nuclear capable.
Iran insists its nuclear programme is for peaceful purposes.
Obama's trip to Jordan was the final stop on a four-day visit to the Middle East that included his first stop in Israel as President.
- AP
