She did not apologize for any British actions during the bitter conflicts between the two neighbors but said it is clear mistakes were made.
"To all those who have suffered as a consequence of our troubled past I extend my sincere thoughts and deep sympathy," she said at a state dinner hosted by Irish President Mary McAleese. "With the benefit of historical hindsight we can all see things which we would wish had been done differently or not at all."
The queen, whose visit has been highlighted by memorable scenes of friendship and forgiveness, emphasized the positive in the rest of her brief speech, saying no one in past centuries could have imagined the bonds of friendship that now unite England and Ireland.
She proposed a toast to the people of Ireland, then said, "I love these clinking glasses," after the champagne flutes were raised and clinked.
Her speech may disappoint those who wanted a formal apology from the British monarch, but others will feel she came quite close to acknowledging British misdeeds in the fight against the Irish independence movement.
The speech marks her only scheduled comments during a planned four-day visit to Ireland — the first every to the republic by a reigning British monarch.
Her journey of reconciliation also took her Wednesday to the site of a notorious massacre where British troops killed 14 Irish civilians in 1920. The large sports stadium is a revered spot for Irish nationalists who mourn those who died there during the conflict with Britain.
This was the site of the original "Bloody Sunday," a day when British forces opened fire on civilians at a major sporting match between Dublin and Tipperary. It has never been forgotten, but the queen's visit was seen by some as a step toward healing.
"I suppose I never thought this would happen, but I hoped," said Tadhg Meehan, a secretary of the Gaelic Athletic Association that hosted the queen's visit.
In a brief talk at the Hogan Room inside the stadium, Gaelic Athletic Association President Christy Cooney welcomed the queen and her husband, Prince Philip.
He mentioned the people who died at the stadium on Bloody Sunday, but he also emphasized the warm relations that now exist between the two countries.
Nickey Brennan, a past president of the association, said the queen's presence at the massacre site would resonate throughout Ireland.
"To have Her Majesty here today is a very important milestone," he said. "It shows how much we've all moved on."
Queen Elizabeth II's decision to make an appearance in Croke Park was part of her larger plan to use this trip to show understanding of the issues that have often separated these two neighboring countries.
Not every stop was so fraught.
The queen and Philip began the day with a visit to the Guinness Storehouse, one of Ireland's most popular sites, and its famous Gravity Bar, which offers a panoramic view of Dublin.
Master brewer Fergal Murray expertly prepared a pint of Guinness for the queen in the Gravity Bar, but she declined after smiling broadly. Philip gazed at the brew with obvious longing but also walked away without a taste.
Earlier, he had joked with Murray, "Is it made with Liffey water?" referring to the nearby river.
The Guinness tour struck a light note on an otherwise serious visit. The queen, in an ivory outfit with oversize blue buttons that matched her hat, went directly from the Guinness building for a meeting with Irish Prime Minister Enda Kenny.
British Prime Minister David Cameron also traveled to Dublin on Wednesday for a meeting with Kenny and to attend the state dinner.
Before the dinner, Cameron said the queen's visit has already been a huge success.
"I think everyone back in the UK has been very struck by the pictures and the scenes and the warm welcome that she's had, and I think this visit will set the seal on what is already a very strong relationship between our two countries, but a relationship I believe that can get even stronger still," he said.
The dinner guests at the historic Dublin Castle feasted on delicacies including cured salmon, rib of Slaney Valley beef with smoked champ potato and fried spring cabbage, and strawberries and cream, a dessert often associated with the Wimbledon tennis championships. Several French wines were served.
The queen was dressed in a white ensemble set off by a spectacular diamond tiara, necklace and earring combination. The Irish president wore a striking blue dress; both of their husbands wore tuxedos.
The guests included Nobel Prize-winning poet Seamus Heaney and a host of prominent politicians, including British Foreign Minister William Hague and Cabinet Secretary Gus O'Donnell, Northern Ireland First Secretary Peter Robinson, former Irish Prime Minister Bertie Ahern as well as Cardinal Sean Brady.
The queen and McAleese also laid wreaths at the Irish National War Memorial Garden on Wednesday, much as they did the day before at the Garden of Remembrance honoring Irish rebels who fought against British rule.
The queen is receiving high marks from the Irish press for her dignified conduct during her long-anticipated visit.
The Irish Daily Mail noted the widespread respect for the queen's decision to honor Ireland's rebels on her first day in Dublin by laying a wreath at the Garden of Remembrance.
"With one momentary bow of the head, Queen Elizabeth II banished centuries of mistrust yesterday in a historic first visit to the Republic of Ireland by a reigning British monarch," wrote journalist Senan Molony.
Despite the friendly welcome, the queen is still being protected by an exceptionally large security contingent of more than 8,500 police backed by troops.
Dissident groups have said disruptions are possible.
On Thursday, the queen plans to visit the Irish National Stud to indulge her love of horses. She also hosts a gala dinner for Irish dignitaries Thursday evening before traveling to Cork on Friday.