Rajapakse ordered the suspension in fighting after intense international pressure, including repeated calls from the United Nations and the US and protests held in cities across Europe.
Ban Ki-moon, the UN secretary-general, welcomed the halt in fighting, but said it fell short of his expectations.
"This is less than the full humanitarian pause of several days I had pressed for, but is nevertheless a useful first step and an opportunity to move towards the peaceful and orderly end to the fighting now so badly needed," he said.
The UN says that more than 100,000 people are trapped with the Tamils in a government-declared "no-fire'' zone.
The Sri Lankan military said last month that more than 50,000 civilians have escaped the conflict zone since January, but has accused the the Liberation Tigers of Tamil Eelam (LTTE) of preventing more from leaving.
The LTTE has insisted that civilians are staying in the area by choice and has repeatedly accused the military of firing into the zone.
The Sri Lankan military denies shooting into civilian areas, saying the allegations are Tiger propaganda and accuses the LTTE of holding civilians hostage.
Call for surrender
In recent months, the government has intensified its campaign against the Tigers and insists the LTTE is close to being defeated.
Announcing the two-day suspension to the military campaign, Rajapaksa also reiterated his call for the LTTE to surrender.
"In the true spirit of the season, it is timely for the LTTE to acknowledge its military defeat and lay down its weapons and surrender. The LTTE must also renounce terrorism and violence permanently," the president said in a statement said.
Mediators of Sri Lanka's peace process - the US, UK, Norway and Japan - on Friday urged the Tigers to end the conflict and urged the military not to fire into the no-fire zone.
The Tigers have been fighting since 1983 for an independent state in the north and east of the island for the Tamil minority, saying Tamils have suffered decades of marginalisation at the hands of governments dominated by the Sinhalese majority.
More than 70,000 people have been killed in the unresolved conflict to date.