Although I find the Big Villain plot very tiresome myself, it must be remembered that if not for the return of Khan in TWoK - featuring the first Trek battle scenes since "Elaan of Troyius" in December 1968 - none of us would likely be here on this BBS.
In live action, the Klingons and V'GER battled in TMP.
Perhaps you mean a battle involving the Enterprise
? TAS had plenty of space battles. And while it's true that there weren't a lot of ship-to-ship space battles in the third season of TOS, The Tholian Web
has a higher production number than Elaan of Troyius.