For example, Sam Shepard played Chuck Yeager in The Right Stuff. Sam died last month, but Chuck is still going. That’s a pretty unusual situation, but it can’t be unique, right? What are some other examples?
Heath Ledger as “Robbie Clark,” which is a persona of Bob Dylan in I’m Not There, but I’m not sure it qualifies.
In Lords of Dogtown Heath Ledger (died 2008) played Skip Engbloom who is still alive.
Patch Adams and Oliver Sacks both survived Robin Williams.
Also Williams played Adrian Cronauer (Good morning Vietnam) who is still alive.
Bobby Watson played Adolf Hitler nine times, starting in 1942. Watson died in 1965.
Uhh… you know some shit that we don’t about Hitler?
If you believe sportswriter Fred Leib’s claim that the character Walter Brennan played in “Pride of the Yankees” to be true (and they are reasonable), then Leib outlived Brennan by six years
I’ll never tell. 
Ron Silver, who died in 2009, portrayed attorney Alan M. Dershowitz in Reversal of Fortune (1990), Henry Kissinger in Kissinger & Nixon (1995), attorney Robert Shapiro in American Tragedy (2000), and Muhammad Ali’s trainer Angelo Dundee in Ali (2001). Dundee passed away in 2012; the rest are still alive.
The character of Alex Latourno in 8 Mile is loosely based on Mathers’ real girlfriend/future wife/future ex-wife Kim Scott. Brittany Murphy, who played Alex, died in 2009. Scott is still alive.
Spencer Tracy (died 1967) played Jimmy Doolittle (died 1993) in Thirty Seconds over Tokyo (1944).
Bill Paxton (d.2017) portrayed Apollo 13 astronaut Fred Haise, who is still alive.
Here’s a twofer. Robert Taylor (died 1969) and Barry Nelson (died April 2007) both played Paul Tibbets (died November 2007) in, respectively, Above and Beyond (1952) and The Beginning of the End (1947).
Another “based on” character: Chance Buckman in Hellfighters was based on Red Adair. John Wayne, who played Buckman, died in 1979. Adair, who served as an advisor on the movie, died in 2004.
Jason Robards (died 2000) played Ben Bradlee (died 2014) in All the President’s Men (1976)
Do parodists count? Phil Hartman (d. 1998) played Ronald Reagan (d. 2004), Bill Clinton (living), Charlton Heston (d. 2008), Jack Nicholson (living), and many others on Saturday Night Live.
I found six in a 1950 bio-ic film “The Jackie Robinson Story” where baseball player Jackie Robinson plays himself. Minor Warson played Branch Rickey; Watson died in July 1965 and Rickey in December. Ruby Dee (died 2014) played Robinson’s wife Rachel, who is still alive at 95. Harry Shannon (1964) played Frank Shaughnessy (1969) who was President of the minor league International League. Joel Fluellen (1990) played Robinson’s older brother Mack (2000). Billy Wayne (1970) played Clyde Sukeforth (2000), the scout who signed Robinson to a Dodgers contract.
Louise Beavers (1964) played Robinson’s mother Mallie (1968).
Anthony Perkins, who played baseball player Jimmy Piersall in *Fear Strikes Out *in 1957, died in 1992. Piersall died in 2017.
A lot of people who have portrayed Fidel Castro (Died November 25, 2016)
Going off IMDB
Night Train to Mundo Fine (1966) Played by Anthony Cardoza (7 December 2015)
Che! (1969) Played by Jack Palance (10 November 2006)
Revolutions: Fidel Castro (1970) Played by Bernard Horsfall (28 January 2013)
The Disciples (1999) (TV) Played by Armando Roblan (9 January 2013)