He laid a wreath at the Innocent Victims Memorial before reading from the Bible at the church.
He gathered with survivors and families affected by the two atrocities in 2015.
Thirty Britons were among 38 people massacred in the Tunisian resort town of Sousse in June last year - the worst incident of terrorism involving British people since the July 7th attacks in London in 2005.
Gunman Seifeddine Rezgui targeted holidaymakers on the beach and in a hotel before being shot dead by security forces. Terror group Islamic State (IS) claimed responsibility.
During the service, Harry and the Prime Minister both read Bible passages, from Revelations and Isaiah respectively, before the 900-strong congregation.
The prince read Revelation 21: 1-7.
The Dean of Westminster, the V Revd Dr John Hall, led the service. He said: "We remember with thanksgiving those whose lives were brutally cut short.
"We honour the courage of those who survived and the families of those who suffered.
"We share our grief with victims of attacks from other countries and their families."
He said many of those attending sought the answer as to why the attacks happened, adding he did not believe the deaths were fated or were "an act of God".
"People have to choose and have the freedom to choose. Some will follow the way of light and peace. Tragically others will follow the way of darkness and destruction," he said.
"Our prayer today is for the defeat of darkness and destruction and that light and peace may have the victory."
The congregation sang the National Anthem to draw the memorial to a close.
The Government is to fund a permanent memorial dedicated to the victims of the Tunisian beach massacre, as well as creating a separate site of remembrance for all British nationals killed in terrorist atrocities overseas.