Naming a 28-strong squad, Southgate also handed a first call-up to Bournemouth's in-form striker Callum Wilson, a recall to Everton defender Michael Keane, and retained Dortmund's Jadon Sancho.
"It's a shame because we want it to be a fitting tribute to an outstanding player who has often, I think, been undervalued in terms of how well he played for England", he said. Wayne is one the greatest ever players to play for England, the greatest goalscorer to play for England, so why not give him the send-off he deserves?
The 33-year-old Rooney, now playing in Major League Soccer with DC United, has not played for England in nearly two years. The fact is it is an opportunity to pay tribute to what he has achieved.
"I've not spoken to Gareth (Southgate) too much about how he's going to do it when we play but it'll be great to see him again and I'm sure he's looking forward to seeing a few of the boys".
Southgate has not had any direct dealings with Rooney since he visited St George's Park in April in his role as an ambassador for last summer's European Under-17 Championship, which goes some way towards explaining some of the confusion that has surrounded his surprise return.
Goalkeeper Peter Shilton, who with 125 caps is the only player to have represented England more times than Rooney, and ex-captain Alan Shearer both agreed that Rooney's achievements deserve honouring - but that should not extend to him playing in the match. "We've not been brilliant at that over the years".
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"I understand that has caused a lot of debate and conjecture but for me I think it is a small way of appreciating what he has done for his country". I thought the Podolski situation was a super night.
He said: "I like Wayne, I get on well with him and his record speaks for itself".
"If we're also talking about helping young players develop in the worldwide set-up, then surely celebrating Wayne's career in this way is an example to the next generation of England stars".
World Cup runners-up Croatia are in last place in League A Group 4, having played a game less than group leaders Spain and England.
"Part of being a footballer is showing the resilience that would be commonplace among the squad, coming back form setbacks whether that's through rejection or injury", said Southgate.