The detective said: "Thank Lewis for me" - a reference to his ever-loyal sidekick Sergeant Lewis.
The final episode, The Remorseful Day, drew 50% of the TV audience, who heard the last words of Morse, played by John Thaw, before he died.
The detective said: "Thank Lewis for me" - a reference to his ever-loyal sidekick Sergeant Lewis.
In an emotional final scene, Lewis, played by Kevin Whately, visited Morse in a mortuary and planted a kiss on his forehead.
ITV was hoping for up to 18 million viewers for the final episode to match the popularity of the series at its peak.
But the programme was competing with international football, a new series of the X-Files on BBC Two and the start of Sir David Attenborough's new landmark series, State of the Planet, on BBC One.
The documentary series, which looks at the precarious future for some of the world's species of animal and wildlife, drew 4 million viewers, and took a 16% share of the audience.
John Thaw, who watched the final programme at home in west London with his wife, actress Sheila Hancock, and his three daughters, said he was delighted with the viewing figures.
He said: "It is marvellous to go out and have people still watching in those numbers after 13 years."
The actor left the room before the final scenes of the programme when his youngest daughter, Jo, began to cry.
A spokesman for Carlton televison said: "It was a great night for ITV and a great climax to 13 years of Morse."
In total, Morse made 33 television investigations, solving more than 80 murders.
A world-wide audience of one billion across 200 countries have seen the detective at work, according to ITV.
Colin Dexter, who wrote the original Morse books, decided to kill off his most famous character after 25 years.
The detective made his debut in a 1975 novel.