Yes, you can.
The Companion keyword only functions outside of the game. This means that if a card with Companion is in your deck, whether as a Commander or just any regular card, then the Companion part of the card doesn't do anything; it's just a normal creature. In the case of a Commander deck, it would just be a normal Legendary Creature which is therefore valid as your Commander.
702.138a Companion is a keyword ability that functions outside the game. It’s written as “Companion—[Condition].” Before the game begins, you may reveal one card you own from outside the game with a companion ability whose condition is fulfilled by your starting deck. (See rule 103.1b.) If you do, once during that game, you may play that card from outside the game.
903.3. Each deck has a legendary creature card designated as its commander. This designation is not a characteristic of the object represented by the card; rather, it is an attribute of the card itself. The card retains this designation even when it changes zones.
Jegantha, the Wellspring is a legendary creature, therefore it can be your Commander.