Now that He has commissioned them, Jesus gives them what they will need to discharge their commission.

The word “breathed” is the same word as in Septuagint of (Gen 2:7) where God breathed the breath of life into Adam, thus indicating a new creation and in (Ezek 37:9) where life is again prophesied to be brought about by the breath of God, but this time from those who were dead. The coming of the Spirit brings both of these: life where there never was any and life to those who were dead (Job 33:4, 2 Cor 5:17).

Genesis 2:7  the LORD God formed the man from the dust of the ground and breathed into his nostrils the breath of life, and the man became a living being.

Ezekiel 37:9  Then he said to me, “Prophesy to the breath; prophesy, son of man, and say to it, ‘This is what the Sovereign LORD says: Come from the four winds, O breath, and breathe into these slain, that they may live.’”

Job 33:4  The Spirit of God has made me; the breath of the Almighty gives me life.

2 Corinthians 5:17  Therefore, if anyone is in Christ, he is a new creation; the old has gone, the new has come!

The words “on them” are not in most manuscripts (actually they are only in one). Jesus just expelled a deep breath on the group in general and did not breathe out upon each individual in turn. The gift Jesus is giving is not a series of gifts to individuals, but a collective gift to the whole church. Though Thomas was not present, the Holy Spirit would not have had a difficult time in finding him so that he could also receive this gift (Num 11:26).

Numbers 11:26  However, two men, whose names were Eldad and Medad, had remained in the camp. They were listed among the elders, but did not go out to the Tent. Yet the Spirit also rested on them, and they prophesied in the camp.

The Holy Spirit is still received by all who accept salvation through the substitutionary death of Christ (1 Cor 6:19, Eph 1:13).

1 Corinthians 6:19  Do you not know that your body is a temple of the Holy Spirit, who is in you, whom you have received from God? You are not your own;

Ephesians 1:13  And you also were included in Christ when you heard the word of truth, the gospel of your salvation. Having believed, you were marked in him with a seal, the promised Holy Spirit,

After the giving of the Spirit in this verse, Jesus later told His disciples to wait for the gift of the Spirit Who would give them power to be witnesses (Luke 24:49, Acts 1:4-5, 8). This other giving of the Holy Spirit would not come until after the ascension of Christ (John 14:16, 26; 16:7, 13) and  was fulfilled on the Day of Pentecost (Acts 2:1-4). This outpouring of the Holy Spirit is proof to us that Christ died, was resurrected, ascended to heaven, and is now seated at the right hand of God (Acts 2:32-36). Pentecost proves the Lordship of Christ.

Luke 24:49  I am going to send you what my Father has promised; but stay in the city until you have been clothed with power from on high.”

Acts 1:4-5  On one occasion, while he was eating with them, he gave them this command: “Do not leave Jerusalem, but wait for the gift my Father promised, which you have heard me speak about.  For John baptised with water, but in a few days you will be baptised with the Holy Spirit.”

Acts 1:8  But you will receive power when the Holy Spirit comes on you; and you will be my witnesses in Jerusalem, and in all Judea and Samaria, and to the ends of the earth.”

John 14:16  And I will ask the Father, and he will give you another Counsellor to be with you for ever—

John 14:26  But the Counsellor, the Holy Spirit, whom the Father will send in my name, will teach you all things and will remind you of everything I have said to you.

John 16:7  But I tell you the truth: It is for your good that I am going away. Unless I go away, the Counsellor will not come to you; but if I go, I will send him to you.

John 16:13  But when he, the Spirit of truth, comes, he will guide you into all truth. He will not speak on his own; he will speak only what he hears, and he will tell you what is yet to come.

Acts 2:1-4  When the day of Pentecost came, they were all together in one place.  Suddenly a sound like the blowing of a violent wind came from heaven and filled the whole house where they were sitting.  They saw what seemed to be tongues of fire that separated and came to rest on each of them.  All of them were filled with the Holy Spirit and began to speak in other tongues as the Spirit enabled them.

Acts 2:32-36  God has raised this Jesus to life, and we are all witnesses of the fact.  Exalted to the right hand of God, he has received from the Father the promised Holy Spirit and has poured out what you now see and hear.  For David did not ascend to heaven, and yet he said, “‘The Lord said to my Lord: “Sit at my right hand  until I make your enemies a footstool for your feet.”’  “Therefore let all Israel be assured of this: God has made this Jesus, whom you crucified, both Lord and Christ.”

These two instances of the giving of the Holy Spirit to the disciples were for two separate things. The first was what all Christians experience when we get saved and was a guarantee of our salvation and the second was for the power to be effective witnesses for Christ. The first is part of the gift of salvation and will always be received when salvation is received. The second is a separate gift and must be received separately, although it may also come at salvation. All gifts must be willingly received, whether they are salvation or empowering by the Holy Spirit.