Howley performed a similar task in 2012-13 when Gatland took a sabbatical to guide the Lions to a 2-1 series win against Australia.
"I'm excited to have the challenge once again," said Howley.
Welsh Rugby Union chief executive Martyn Phillips said: "Rob represents the optimum appointment for Wales."
In a WRU statement, Gatland said: "Rob's appointment is great news for the squad."
"We have an experienced management team in place and Rob's international experience as a coach and his desire to continue developing is a great mix to drive the squad forward."
Howley's primary target is to ensure Wales are as highly-ranked as possible by May, 2017 when the 2019 Rugby World Cup (RWC) draw will take place.
Wales go into 2016-17 in fifth place, with Australia, South Africa, England and New Zealand above them and Ireland a place below.
Wales went into the 2015 World Cup facing hosts England and Australia in their pool having slipped out of the world's top eight two days before the seedings for that event were finalised.
Howley said: "The 2019 RWC seedings will be decided upon post-2017 Six Nations, so each match is vitally important to us looking forward and ahead to that competition."
He deputised for Gatland when the latter's broken heels meant he could not make Wales' 2012 tour to Australia.
After Gatland was named 2013 Lions coach in Sept 2012, Howley's role as caretaker was extended to cover the 2013 Six Nations.
That ended with a record 30-3 win over England as Wales won European rugby's crown.
Before their 2017 Six Nations begins against Italy in Cardiff on 5 February, Wales host Australia, Argentina, Japan and South Africa on successive Saturdays in November.
Robert Howley will deputise for Wales coach Warren Gatland, who is taking charge of the 2017 British and Irish Lions tour to New Zealand.